5O9D

Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43H, H39Y


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829317% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mg/ml ADH-A
Crystal Properties
Matthews coefficientSolvent content
2.3647.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.492α = 90
b = 104.828β = 91.13
c = 109.009γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.7928.31990.1140.0720.9916.73.413747513.2
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)
11.791.82900.6720.4410.5731.53.1

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 REPLACEMENTTHROUGHOUT3jv71.7928.3130487689299.230.171340.17030.19131RANDOM23.03
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]
0.640.70.2-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.759
r_dihedral_angle_4_deg14.943
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg5.729
r_long_range_B_other5.144
r_long_range_B_refined5.143
r_angle_refined_deg1.46
r_scangle_other1.141
r_angle_other_deg0.927
r_mcangle_it0.787
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.759
r_dihedral_angle_4_deg14.943
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg5.729
r_long_range_B_other5.144
r_long_range_B_refined5.143
r_angle_refined_deg1.46
r_scangle_other1.141
r_angle_other_deg0.927
r_mcangle_it0.787
r_mcangle_other0.787
r_scbond_it0.7
r_scbond_other0.692
r_mcbond_it0.45
r_mcbond_other0.45
r_chiral_restr0.076
r_bond_refined_d0.009
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 Atoms9873
Nucleic Acid Atoms
Solvent Atoms1208
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing