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Crystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.01M cobalt chloride, 1.80M ammonium sulfate, 0.1M MES pH 6.5, Additive - 0.001 M 3-oxo-delta 4,6, Lithocholyl Coenzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.956 α = 90 b = 52.956 β = 90 c = 428.627 γ = 120
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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 2.2 28.575 98.5 0.086 12.88 12340 -3 39.357
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 2.2 2.28 94.1 0.479 2.9 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4L8P 2.2 28.575 11786 568 94.73 0.1958 0.1942 0.225 0.2124 RANDOM 35.1609
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] 0.11 0.11 0.11 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_dihedral_angle_4_deg 15.092 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 6.472 r_mcangle_it 3.882 r_mcbond_it 2.454 r_mcbond_other 2.404 r_angle_refined_deg 1.319 r_angle_other_deg 0.849 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_dihedral_angle_4_deg 15.092 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 6.472 r_mcangle_it 3.882 r_mcbond_it 2.454 r_mcbond_other 2.404 r_angle_refined_deg 1.319 r_angle_other_deg 0.849 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1335 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 23
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction PHASER phasing XSCALE data scaling REFMAC refinement XDS data reduction