5O8H

Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, F43H, H39Y


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JV7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829319% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 20 mM MgCl2, 150 mM NaCl, 7.5 mg/ml ADH-A
Crystal Properties
Matthews coefficientSolvent content
2.4248.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.702α = 90
b = 105.678β = 91.51
c = 109.623γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.9629.6399.60.1030.0650.9956.93.410761824.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.961.9993.70.7640.4890.5741.53.3

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 REPLACEMENTTHROUGHOUT3jv71.9629.63102015519099.890.1770.175630.20352RANDOM32.466
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]
-0.710.211-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.591
r_dihedral_angle_4_deg17.395
r_dihedral_angle_3_deg12.103
r_dihedral_angle_1_deg5.74
r_long_range_B_other5.687
r_long_range_B_refined5.686
r_scangle_other3.519
r_mcangle_it2.74
r_mcangle_other2.74
r_scbond_it2.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.591
r_dihedral_angle_4_deg17.395
r_dihedral_angle_3_deg12.103
r_dihedral_angle_1_deg5.74
r_long_range_B_other5.687
r_long_range_B_refined5.686
r_scangle_other3.519
r_mcangle_it2.74
r_mcangle_other2.74
r_scbond_it2.263
r_scbond_other2.263
r_mcbond_it1.859
r_mcbond_other1.859
r_angle_refined_deg1.448
r_angle_other_deg0.942
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms9877
Nucleic Acid Atoms
Solvent Atoms1122
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing