3G0I

Complex of Aspergillus niger epoxide hydrolase with valpromide (2-propylpentanamide)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QO7PDB ENTRY 1QO7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629320% PEG6000, 0.1M MES, pH6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.985α = 90
b = 89.655β = 105.31
c = 75.812γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r1999-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9763ESRFID14-4

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
12.14099.50.06616.94747596
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)
2.12.1492.80.2132189

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QO72.138.214749847296121499.580.1760.1760.1750.222RANDOM14.057
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]
-0.02-0.030.1-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_4_deg17.375
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.862
r_scangle_it2.283
r_scbond_it1.441
r_angle_refined_deg1.189
r_mcangle_it0.931
r_mcbond_it0.563
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_4_deg17.375
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.862
r_scangle_it2.283
r_scbond_it1.441
r_angle_refined_deg1.189
r_mcangle_it0.931
r_mcbond_it0.563
r_nbtor_refined0.307
r_nbd_refined0.187
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.128
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6218
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms20

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction