4L8O

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L8P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.01M 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 coefficientSolvent content
2.657.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.956α = 90
b = 52.956β = 90
c = 428.627γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315KOHZU: Double Crystal Si(111)2012-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.228.57598.50.08612.8812340-339.357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2894.10.4792.94.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4L8P2.228.5751178656894.730.19580.19420.225RANDOM35.1609
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]
0.110.110.11-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg15.092
r_dihedral_angle_3_deg13.712
r_dihedral_angle_1_deg6.472
r_mcangle_it3.882
r_mcbond_it2.454
r_mcbond_other2.404
r_angle_refined_deg1.319
r_angle_other_deg0.849
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg15.092
r_dihedral_angle_3_deg13.712
r_dihedral_angle_1_deg6.472
r_mcangle_it3.882
r_mcbond_it2.454
r_mcbond_other2.404
r_angle_refined_deg1.319
r_angle_other_deg0.849
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1335
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms23

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction