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Crystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.3 α = 90 b = 49.9 β = 90 c = 118.2 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 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 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 1.76 29.553 94.1 0.087 0.082 21.72 8.1 25719 5.5 27.8
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 1.76 2 96.4 0.37 0.306 5.55 5 7021
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 1C1H 1.8 29.55 25617 1281 100 0.194 0.192 0.19 0.25 0.2475 RANDOM 25.116
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] 0.81 -1.37 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.329 r_dihedral_angle_4_deg 14.999 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 5.201 r_scangle_it 3.042 r_scbond_it 2.055 r_angle_refined_deg 1.525 r_mcangle_it 1.2 r_mcbond_it 0.764 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.329 r_dihedral_angle_4_deg 14.999 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 5.201 r_scangle_it 3.042 r_scbond_it 2.055 r_angle_refined_deg 1.525 r_mcangle_it 1.2 r_mcbond_it 0.764 r_nbtor_refined 0.299 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2486 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ProDC data collection XDS data reduction XDS data scaling PHASER phasing