6T92

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH and the substrate formate at a secondary site.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DNA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52910.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 10 % w/v PEG 1000, 10 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.4549.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.731α = 85.627
b = 94.606β = 89.88
c = 94.614γ = 81.618
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.1263.9382.10.9985.71.754821315.7
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)
11.121.1453.20.2910.81.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE5dna1.1263.935482122733182.1010.2080.20690.227618.109
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]
-0.172-0.052-0.0410.7930.069-0.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.156
r_dihedral_angle_4_deg14.201
r_dihedral_angle_3_deg13.08
r_dihedral_angle_1_deg6.819
r_lrange_other6.113
r_lrange_it6.112
r_scangle_it5.084
r_scangle_other5.083
r_scbond_it3.963
r_scbond_other3.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.156
r_dihedral_angle_4_deg14.201
r_dihedral_angle_3_deg13.08
r_dihedral_angle_1_deg6.819
r_lrange_other6.113
r_lrange_it6.112
r_scangle_it5.084
r_scangle_other5.083
r_scbond_it3.963
r_scbond_other3.963
r_mcangle_it3.785
r_mcangle_other3.785
r_mcbond_it3.013
r_mcbond_other3.013
r_angle_other_deg2.339
r_angle_refined_deg1.92
r_symmetry_nbd_refined0.253
r_nbd_other0.248
r_symmetry_xyhbond_nbd_refined0.248
r_nbd_refined0.216
r_symmetry_nbd_other0.212
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.163
r_xyhbond_nbd_other0.135
r_chiral_restr0.103
r_ncsr_local_group_50.074
r_ncsr_local_group_60.072
r_symmetry_nbtor_other0.071
r_ncsr_local_group_40.069
r_ncsr_local_group_10.066
r_ncsr_local_group_20.066
r_ncsr_local_group_30.063
r_bond_other_d0.034
r_gen_planes_other0.032
r_gen_planes_refined0.018
r_bond_refined_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11503
Nucleic Acid Atoms
Solvent Atoms1759
Heterogen Atoms256

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing