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Crystal Structure of B. subtilis ferrochelatase with Cobalt bound at the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DOZ PDB ENTRY 1DOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG 2000, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.41 α = 90 b = 49.9 β = 90 c = 118.08 γ = 90
Symmetry Space Group P 21 21 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 CCD MAR CCD 165 mm 2009-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.94 30 99.9 0.099 13.5 40865 40865
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.94 1.99 100 0.507 6.19 13.5 2994
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 PDB ENTRY 1DOZ 1.94 20 20726 1117 99.99 0.16995 0.1684 0.1695 0.19854 0.199 RANDOM 18.813
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] 0.29 -1.24 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 23.3 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 4.976 r_scangle_it 4.144 r_scbond_it 2.367 r_mcangle_it 1.413 r_angle_refined_deg 1.248 r_mcbond_it 0.708 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 23.3 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 4.976 r_scangle_it 4.144 r_scbond_it 2.367 r_mcangle_it 1.413 r_angle_refined_deg 1.248 r_mcbond_it 0.708 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2483 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 6
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling