3BHM

Crystal structure of human Carbonyl Reductase 1 in complex with S-hydroxymethylglutathione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WMAPDB ENTRY 1WMA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298vapor diffusion, hanging drop, temperature 298K, pH7.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.158α = 90
b = 55.943β = 90
c = 95.274γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.665097.10.04910.95.734423
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)
1.661.7281.80.5683.22858

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WMA1.848.2227565138399.070.1720.1710.206RANDOM17.469
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]
-0.370.080.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.405
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg11.694
r_dihedral_angle_1_deg5.156
r_scangle_it2.819
r_scbond_it1.853
r_angle_refined_deg1.346
r_mcangle_it1.232
r_mcbond_it0.772
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.405
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg11.694
r_dihedral_angle_1_deg5.156
r_scangle_it2.819
r_scbond_it1.853
r_angle_refined_deg1.346
r_mcangle_it1.232
r_mcbond_it0.772
r_nbtor_refined0.303
r_nbd_refined0.197
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.116
r_xyhbond_nbd_refined0.115
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2035
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms132

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection