4US8

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with benzaldehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VLBPDB ENTRY 1VLB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.6277VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. ISOPROPANOL WAS REMOVED AND CRYSTAL WAS SOAKED WITH 1.4MM BENZALDEHYDE FOR 1H.
Crystal Properties
Matthews coefficientSolvent content
2.4750.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.229α = 90
b = 143.229β = 90
c = 162.25γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS PILATUS 6M2011-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.49124.0499.70.0420.45.71582222
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)
11.491.521000.2276.5

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 1VLB1.49124.04150228793099.630.092640.091090.12215RANDOM14.121
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]
0.190.090.19-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.613
r_dihedral_angle_2_deg35.902
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg11.756
r_sphericity_bonded10.072
r_dihedral_angle_1_deg6.456
r_rigid_bond_restr2.59
r_angle_refined_deg1.999
r_scbond_it1.699
r_mcangle_it1.538
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.613
r_dihedral_angle_2_deg35.902
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg11.756
r_sphericity_bonded10.072
r_dihedral_angle_1_deg6.456
r_rigid_bond_restr2.59
r_angle_refined_deg1.999
r_scbond_it1.699
r_mcangle_it1.538
r_mcbond_it1.123
r_mcbond_other1.122
r_angle_other_deg0.913
r_chiral_restr0.096
r_gen_planes_other0.023
r_bond_other_d0.014
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6815
Nucleic Acid Atoms
Solvent Atoms1270
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing