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Crystal structure of the Tyr13Met variant of Bacillus subtilis ferrochelatase
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, HANGING DROP 7.4 298 25-30 % PEG 2000, 0.2 M MgCl2, 0.1 M TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.33 α = 90 b = 49.9 β = 90 c = 118.05 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 MARMOSAIC 225 mm CCD mirrors 2005-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 0.97935 MAX II I911-5
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 1.6 25 97.7 0.102 0.107 13 7.1 37676 37676
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 93.7 0.418 0.236 4.6 7.3 5739
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.6 24.17 35770 35770 1883 100 0.19953 0.19953 0.19775 0.2029 0.23246 0.236 RANDOM 10.409
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] -0.42 -0.26 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.564 r_dihedral_angle_4_deg 20.919 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_1_deg 5.071 r_scangle_it 4.229 r_scbond_it 2.559 r_mcangle_it 1.459 r_angle_refined_deg 1.374 r_angle_other_deg 0.889 r_mcbond_it 0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.564 r_dihedral_angle_4_deg 20.919 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_1_deg 5.071 r_scangle_it 4.229 r_scbond_it 2.559 r_mcangle_it 1.459 r_angle_refined_deg 1.374 r_angle_other_deg 0.889 r_mcbond_it 0.756 r_mcbond_other 0.217 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2464 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345dtb data collection XDS data reduction XSCALE data scaling CNS phasing