☰ Navigation Tabs
A reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ and sirohydrochlorin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1M ammonium sulfate, 0.3M Na-formate, 0.1M Na-acetate, 3% (w/v) gamma-PGA, 5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.97 58.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.88 α = 90 b = 68.88 β = 90 c = 83 γ = 90
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 EIGER X 16M 2019-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.485766 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.1 48.71 99.7 0.117 0.122 0.998 16.3 12.831 7105 92.576
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 100 0.931 0.967 0.83 3.01 13.761
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 2XWS 3.1 48.71 6748 356 99.72 0.1732 0.1708 0.1716 0.2194 0.2199 RANDOM 97.846
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] 0.04 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.925 r_dihedral_angle_3_deg 22.997 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_1_deg 6.426 r_angle_refined_deg 1.97 r_chiral_restr 0.124 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1888 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing