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Room temperature crystal structure of PhnD from Synechococcus MITS9220 in complex with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7S6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris pH 8.5, 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.027 α = 90 b = 40.683 β = 92.78 c = 106.513 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.979 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 53.17 99.78 0.116 0.998 14.4 8.7 26032
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.82 97.02 1.387 0.416 1 5.5
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 MOLECULAR REPLACEMENT THROUGHOUT 7S6G 1.8 53.17 24584 1332 99.18 0.15352 0.15131 0.1621 0.19705 0.2009 RANDOM 31.661
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] 0.01 -0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 21.833 r_dihedral_angle_3_deg 14.794 r_long_range_B_refined 8.526 r_long_range_B_other 8.395 r_scangle_other 6.887 r_dihedral_angle_1_deg 6.477 r_scbond_other 4.353 r_scbond_it 4.347 r_mcangle_other 3.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 21.833 r_dihedral_angle_3_deg 14.794 r_long_range_B_refined 8.526 r_long_range_B_other 8.395 r_scangle_other 6.887 r_dihedral_angle_1_deg 6.477 r_scbond_other 4.353 r_scbond_it 4.347 r_mcangle_other 3.645 r_mcangle_it 3.644 r_mcbond_it 2.667 r_mcbond_other 2.661 r_angle_refined_deg 1.629 r_angle_other_deg 1.464 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2125 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction xia2.multiplex data scaling PHASER phasing