1H0H

Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NAPPDB ENTRY 2NAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M HEPES 7.5, 20% PEG 3350 (W/V), 10% ISOPROPANOL (V/V), 1% BETA-OCTYLGLUCOSIDE, 4 DEGREES CELCIUS, HANGING DROPS., pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.6554

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.408α = 90
b = 110.398β = 93.53
c = 156.185γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH1999-11-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.992,1.214,1.735,1.7415ESRFBM14

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
11.835920.07851.9220129
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)
11.81.88700.621.65

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 2NAP1.8352087821097995.70.1690.1670.201RANDOM19.1
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]
-0.430.381.22-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.862
r_dihedral_angle_1_deg4.495
r_scangle_it1.889
r_angle_refined_deg1.563
r_mcangle_it1.502
r_scbond_it1.336
r_mcbond_it0.97
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.244
r_nbd_refined0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.862
r_dihedral_angle_1_deg4.495
r_scangle_it1.889
r_angle_refined_deg1.563
r_mcangle_it1.502
r_scbond_it1.336
r_mcbond_it0.97
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.244
r_nbd_refined0.218
r_xyhbond_nbd_refined0.155
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms18786
Nucleic Acid Atoms
Solvent Atoms1708
Heterogen Atoms288

Software

Software
Software NamePurpose
Omodel building
SCALEPACKdata scaling
SHARPphasing
AMoREphasing
ARP/wARPphasing
Ophasing
REFMACrefinement