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Crystal Structure of B. subtilis ferrochelatase with Iron 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 8 288 25% PEG 2000, 0.2 M MgCl2, 0.1 M Tris-HCl , pH 8.0, VAPOR DIFFUSION, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.65 α = 90 b = 49.98 β = 90 c = 118.85 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 2005-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0605 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 20 100 0.027 0.055 11.3 31884
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.81 95.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1.71 19.64 2 30288 30288 1595 100 0.17824 0.17609 0.1748 0.21951 0.2173 RANDOM 15.516
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] 0.57 -1.03 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 17.977 r_dihedral_angle_3_deg 12.07 r_dihedral_angle_1_deg 4.926 r_scangle_it 3.491 r_scbond_it 2.262 r_angle_refined_deg 1.347 r_mcangle_it 1.295 r_mcbond_it 0.818 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 17.977 r_dihedral_angle_3_deg 12.07 r_dihedral_angle_1_deg 4.926 r_scangle_it 3.491 r_scbond_it 2.262 r_angle_refined_deg 1.347 r_mcangle_it 1.295 r_mcbond_it 0.818 r_nbtor_refined 0.304 r_metal_ion_refined 0.261 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2495 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing