4O9U

Mechanism of transhydrogenase coupling proton translocation and hydride transfer


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 50 mM MgCl2, 0.5 M trimethylamine N-oxide, 26% polyethylenglycol 400, 2% octyl glucoside, 0.1mM NADP, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.33 α = 90
b = 160.59 β = 128.36
c = 139.62 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- --
Diffraction Radiation
Monochromator Protocol
Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
6.93 38.9 98.3 -- -- -- -- 5015 4922 0.0 0.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 6.926 38.9 -- -- -- 4694 228 98.11 -- 0.21598 0.21271 0.28372 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 6.926 7.105 -- 17 298 0.296 0.414 -- 86.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 160.054
Anisotropic B[1][1] -21.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -9.66
Anisotropic B[2][2] -16.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 23.52
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.064
r_bond_refined_d 0.006
r_mcangle_it 9.321
r_angle_refined_deg 1.102
r_dihedral_angle_1_deg 4.964
r_gen_planes_refined 0.004
r_long_range_B_refined 23.161
r_dihedral_angle_4_deg 14.192
r_dihedral_angle_2_deg 37.52
r_mcbond_it 5.088
r_dihedral_angle_3_deg 19.273
r_scbond_it 3.848
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13434
Nucleic Acid Atoms 0
Heterogen Atoms 184
Solvent Atoms 0

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
REFMAC refinement version: 5.8.0049
XDS data reduction
SCALA data scaling