8RCC

W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829322% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.81α = 90
b = 124.401β = 90
c = 150.307γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2022-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.30195.83589.190.98546.555.645048
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.3012.440.465

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.30195.83545013226782.2010.1960.19380.244233.536
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]
0.131-0.007-0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.551
r_dihedral_angle_4_deg18.145
r_dihedral_angle_3_deg16.189
r_dihedral_angle_1_deg7.349
r_lrange_it5.377
r_lrange_other5.377
r_scangle_it3.571
r_scangle_other3.571
r_mcangle_it3.464
r_mcangle_other3.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.551
r_dihedral_angle_4_deg18.145
r_dihedral_angle_3_deg16.189
r_dihedral_angle_1_deg7.349
r_lrange_it5.377
r_lrange_other5.377
r_scangle_it3.571
r_scangle_other3.571
r_mcangle_it3.464
r_mcangle_other3.464
r_scbond_it2.295
r_scbond_other2.292
r_mcbond_it2.239
r_mcbond_other2.237
r_angle_refined_deg1.36
r_angle_other_deg1.145
r_symmetry_nbd_refined0.264
r_nbd_other0.215
r_nbd_refined0.198
r_symmetry_nbd_other0.183
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.148
r_symmetry_nbtor_other0.075
r_chiral_restr0.057
r_symmetry_xyhbond_nbd_refined0.051
r_symmetry_xyhbond_nbd_other0.008
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9199
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms242

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling