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Crystal Structure of Precorrin-8X Methyl Mutase CbiC/CobH from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 JCSG+ condition A2, 20% PEG3000, 0.1 M Na citrate pH 5.5, 0.4/0.4 uL drops, Crystal ID 10993a2, 20 mg/mL protein in 20 mM HEPES pH 7.0, 0.3 M NaCl, 5% glycerol, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.724 α = 90 b = 68.927 β = 95.88 c = 103.196 γ = 90
Symmetry Space Group P 1 21 1
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 300 mm CCD 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 1.8 50 91.7 0.136 21.7 3 67776
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 1.8 1.86 86.8 0.501 2.2 2.5 6377
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 1F2V 1.8 50 67763 3309 91.15 0.234 0.232 0.2381 0.26 0.2395 RANDOM 26.486
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] 1.51 1.76 -1.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.83 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 17.223 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.494 r_scbond_it 1.468 r_angle_other_deg 1.405 r_angle_refined_deg 1.318 r_mcangle_it 0.836 r_mcbond_it 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.83 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 17.223 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.494 r_scbond_it 1.468 r_angle_other_deg 1.405 r_angle_refined_deg 1.318 r_mcangle_it 0.836 r_mcbond_it 0.473 r_mcbond_other 0.187 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5909 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling