4C7Y

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with sodium dithionite and sodium sulfide


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 CRYSTALS WERE SOAKED WITH 30MM SODIUM DITHIONITE AND 7MM SODIUM SULFIDE FOR 24H.
Crystal Properties
Matthews coefficientSolvent content
2.4750

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.25α = 90
b = 143.25β = 90
c = 162.3γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4r2007-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.5725.6899.50.0912.55.31351372
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)
11.571.6599.90.353.84.9

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 1VLB1.57124.06128341679399.320.135570.13440.15792RANDOM15.539
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]
-0.19-0.09-0.190.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.749
r_dihedral_angle_4_deg16.568
r_dihedral_angle_3_deg12.551
r_dihedral_angle_1_deg6.45
r_scbond_it2.391
r_angle_refined_deg1.627
r_mcangle_it1.606
r_mcbond_it1.15
r_mcbond_other1.149
r_angle_other_deg0.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.749
r_dihedral_angle_4_deg16.568
r_dihedral_angle_3_deg12.551
r_dihedral_angle_1_deg6.45
r_scbond_it2.391
r_angle_refined_deg1.627
r_mcangle_it1.606
r_mcbond_it1.15
r_mcbond_other1.149
r_angle_other_deg0.855
r_chiral_restr0.092
r_gen_planes_other0.029
r_bond_other_d0.019
r_bond_refined_d0.011
r_gen_planes_refined0.011
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6815
Nucleic Acid Atoms
Solvent Atoms1232
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing