5UNI

Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE6.52931:1 60 mg/mL protein / 1-(8Z-pentadecenoyl)-rac-glycerol (mixed using a mechanical syringe mixer) in MAG 8.7 and precipitant (30% PEG400, 0.1 M MES, pH 6.5, 0.1-0.4 M magnesium nitrate, 1.0-2.5% benzamidine hydrochloride)
Crystal Properties
Matthews coefficientSolvent content
3.3763.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.858α = 90
b = 108.936β = 90
c = 109.338γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 6M-F2015-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.99APS24-ID-C

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
12.243.34960.06611.52.624963
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.28

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.243.3423658131195.660.188310.186370.22343RANDOM46.375
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]
0.05-0.060.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.893
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg13.746
r_long_range_B_other13.425
r_long_range_B_refined13.417
r_scangle_other8.197
r_dihedral_angle_1_deg5.711
r_mcangle_other5.696
r_mcangle_it5.695
r_scbond_it5.626
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.893
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg13.746
r_long_range_B_other13.425
r_long_range_B_refined13.417
r_scangle_other8.197
r_dihedral_angle_1_deg5.711
r_mcangle_other5.696
r_mcangle_it5.695
r_scbond_it5.626
r_scbond_other5.624
r_mcbond_it3.935
r_mcbond_other3.93
r_angle_refined_deg1.958
r_angle_other_deg1.076
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2607
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing