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Magnesium chelatase H subunit (ChlH) E625K variant from Synechocystis sp.PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 0.8-1.2 M sodium citrate and 2 mM dithiothreitol
Crystal Properties Matthews coefficient Solvent content 3.43 64.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 320.422 α = 90 b = 320.422 β = 90 c = 104.876 γ = 120
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 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.79 80.11 100 0.074 0.993 6.4 5.7 99929
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.86 0.659 0.583 1.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YSG 2.79 80.105 99184 4926 99.25 0.212 0.2089 0.2124 0.2676 0.2669 Random 61.264
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] 1.225 0.612 1.225 -3.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_4_deg 16.515 r_lrange_it 8.812 r_lrange_other 8.812 r_dihedral_angle_1_deg 6.963 r_mcangle_it 6.02 r_mcangle_other 6.02 r_scangle_it 5.778 r_scangle_other 5.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_4_deg 16.515 r_lrange_it 8.812 r_lrange_other 8.812 r_dihedral_angle_1_deg 6.963 r_mcangle_it 6.02 r_mcangle_other 6.02 r_scangle_it 5.778 r_scangle_other 5.777 r_mcbond_it 3.819 r_mcbond_other 3.819 r_scbond_it 3.585 r_scbond_other 3.584 r_angle_refined_deg 1.381 r_angle_other_deg 1.171 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.181 r_nbd_other 0.174 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.153 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19393 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing