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Structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 292 300 mM Na Acetate, 25% PEG2000 MME, 100 mM HEPES buffer, pH 8.0, Vapor diffusion, Temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.13 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.607 α = 90 b = 124.021 β = 90 c = 118.447 γ = 90
Symmetry Space Group C 2 2 21
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 KB mirrors 2015-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 68.7 97.6 0.039 0.038 0.999 14.8 3.4 32084 39.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 96.3 0.384 0.366 0.811 2.5 3.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5NPL 2.15 38.58 30438 1643 97.13 0.18105 0.1783 0.1866 0.23419 0.2343 RANDOM 53.779
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] -2.42 2.24 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.714 r_dihedral_angle_4_deg 15.391 r_dihedral_angle_3_deg 14.84 r_long_range_B_refined 6.202 r_long_range_B_other 6.182 r_dihedral_angle_1_deg 5.961 r_scangle_other 3.273 r_mcangle_it 2.561 r_mcangle_other 2.561 r_scbond_it 1.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.714 r_dihedral_angle_4_deg 15.391 r_dihedral_angle_3_deg 14.84 r_long_range_B_refined 6.202 r_long_range_B_other 6.182 r_dihedral_angle_1_deg 5.961 r_scangle_other 3.273 r_mcangle_it 2.561 r_mcangle_other 2.561 r_scbond_it 1.979 r_scbond_other 1.976 r_angle_refined_deg 1.695 r_mcbond_it 1.606 r_mcbond_other 1.603 r_angle_other_deg 1.016 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4001 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing ARP/wARP model building