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Crystal structure of the Tyr13Phe mutant variant of Bacillus subtilis Ferrochelatase with Zn(2+) 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 7.4 288 PEG 2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2 38.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.17 α = 90 b = 49.7 β = 90 c = 117.97 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 MARRESEARCH 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.079 MAX II I711
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 2.5 20 95.3 0.117 0.102 4 9793 9793 37.3
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) 2.5 2.66 73.7 0.214 0.303 3.3 1339
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 (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 2.5 20 10278 9793 863 95.3 0.21 0.21 0.2213 0.257 0.2565 RANDOM 23.4
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] -6.18 -6.75 12.93
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.81 c_mcangle_it 2.07 c_scbond_it 1.85 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.9 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.81 c_mcangle_it 2.07 c_scbond_it 1.85 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.9 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2485 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement MAR345 data collection XDS data scaling CNS phasing