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The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Morpheus screen condition H12:
Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350;
Buffer system 3: 1.0M Tris (base); bicine, pH 8.5
Additives: amino acids: 0.2M Gly, DL-Ala, DL-Ser, DL-Glu, DL-Lys
Crystal Properties Matthews coefficient Solvent content 2.95 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.695 α = 90 b = 177.726 β = 90 c = 106.372 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97932 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.419 106.372 96.1 0.077 0.082 0.027 0.998 13.8 8.7 383047 19.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.419 1.503 61.3 1.22 1.313 0.478 0.623 1.7 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1B33 1.419 106.372 383047 19133 87.258 0.128 0.1255 0.1406 0.1751 0.1843 25.715
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.04 2.665 -3.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_other_3_deg 30.531 r_dihedral_angle_4_deg 15.71 r_dihedral_angle_3_deg 13.745 r_lrange_it 5.396 r_dihedral_angle_1_deg 4.856 r_lrange_other 4.683 r_scangle_it 3.961 r_scangle_other 3.961 r_scbond_it 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_other_3_deg 30.531 r_dihedral_angle_4_deg 15.71 r_dihedral_angle_3_deg 13.745 r_lrange_it 5.396 r_dihedral_angle_1_deg 4.856 r_lrange_other 4.683 r_scangle_it 3.961 r_scangle_other 3.961 r_scbond_it 3.3 r_scbond_other 3.3 r_mcangle_it 2.914 r_mcangle_other 2.914 r_rigid_bond_restr 2.503 r_mcbond_it 2.392 r_mcbond_other 2.392 r_angle_refined_deg 1.517 r_angle_other_deg 1.489 r_symmetry_nbd_refined 0.262 r_nbd_refined 0.218 r_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.123 r_ncsr_local_group_26 0.113 r_ncsr_local_group_3 0.111 r_ncsr_local_group_4 0.11 r_ncsr_local_group_14 0.108 r_ncsr_local_group_29 0.108 r_ncsr_local_group_13 0.106 r_ncsr_local_group_21 0.104 r_ncsr_local_group_19 0.103 r_ncsr_local_group_18 0.102 r_ncsr_local_group_25 0.102 r_ncsr_local_group_17 0.098 r_ncsr_local_group_15 0.097 r_ncsr_local_group_2 0.096 r_ncsr_local_group_28 0.096 r_ncsr_local_group_11 0.095 r_ncsr_local_group_6 0.094 r_ncsr_local_group_20 0.094 r_ncsr_local_group_27 0.094 r_ncsr_local_group_5 0.093 r_ncsr_local_group_12 0.093 r_ncsr_local_group_1 0.092 r_ncsr_local_group_8 0.09 r_ncsr_local_group_7 0.089 r_ncsr_local_group_9 0.087 r_ncsr_local_group_16 0.087 r_ncsr_local_group_30 0.087 r_chiral_restr 0.084 r_ncsr_local_group_24 0.084 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_22 0.08 r_ncsr_local_group_10 0.075 r_ncsr_local_group_23 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14448 Nucleic Acid Atoms Solvent Atoms 3208 Heterogen Atoms 841
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling autoPROC data scaling STARANISO data scaling PHASER phasing Coot model building