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Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.89 A resolution with product added
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 5 293 10.00% polyethylene glycol 6000, 0.1M citric acid pH 5.0, 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 2.43 49.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.282 α = 90 b = 84.282 β = 90 c = 311.823 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) Rrim I (All) 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 1.89 47.414 99.9 0.069 0.073 19.5 34715 -3 26.185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 98.8 0.885 0.953 0.35 2.5 7.2
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 4L8P 1.89 47.414 34711 1748 99.87 0.1894 0.1879 0.197 0.2183 0.2219 RANDOM 35.823
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] 0.55 0.55 0.55 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.127 r_dihedral_angle_3_deg 12.194 r_dihedral_angle_4_deg 10.436 r_dihedral_angle_1_deg 6.348 r_mcangle_it 4.372 r_mcbond_it 3.334 r_mcbond_other 3.318 r_angle_refined_deg 1.375 r_angle_other_deg 0.823 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.127 r_dihedral_angle_3_deg 12.194 r_dihedral_angle_4_deg 10.436 r_dihedral_angle_1_deg 6.348 r_mcangle_it 4.372 r_mcbond_it 3.334 r_mcbond_other 3.318 r_angle_refined_deg 1.375 r_angle_other_deg 0.823 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2722 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 124
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction PHASER phasing XSCALE data scaling REFMAC refinement XDS data reduction