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Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.85 33.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.836 α = 70.35 b = 38.615 β = 83.05 c = 39.845 γ = 72.09
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 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-01-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915,0.97903,0.91162 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 29.618 96.7 0.054 3.3 25860
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.6 29.618 25860 1291 96.46 0.172 0.17 0.1773 0.209 0.2117 RANDOM 19.754
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] 0.07 -1.08 1.11 1.13 -1.16 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_3_deg 13.339 r_scangle_it 8.55 r_dihedral_angle_1_deg 6.166 r_scbond_it 5.39 r_mcangle_it 3.135 r_mcbond_it 1.918 r_angle_refined_deg 1.645 r_angle_other_deg 1.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_3_deg 13.339 r_scangle_it 8.55 r_dihedral_angle_1_deg 6.166 r_scbond_it 5.39 r_mcangle_it 3.135 r_mcbond_it 1.918 r_angle_refined_deg 1.645 r_angle_other_deg 1.151 r_mcbond_other 0.527 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing