6FG0

Crystal structure of R. ruber ADH-A, mutant Y54G, F43T, L119Y, F282W


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829315% Polyacrylic acid 510 100 mM Tris pH 8 4 mM NAD+ 10 mM MgCl2 3 mg/ml ADHA mutant
Crystal Properties
Matthews coefficientSolvent content
2.3547.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.706α = 90
b = 105.463β = 91.4
c = 108.977γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-07-13MSINGLE 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)Rrim I (All)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
11.7429.594.10.060.070.0360.99811.53.514302518.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.7760.80.5860.7360.4350.6031.42.3

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 REPLACEMENTTHROUGHOUT3jv71.7429.5135478749394.10.163880.162890.18132RANDOM29.156
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]
-1.230.341.120.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.777
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg11.655
r_dihedral_angle_1_deg5.844
r_long_range_B_refined5.338
r_long_range_B_other5.031
r_angle_refined_deg1.481
r_scangle_other1.41
r_mcangle_it1.128
r_mcangle_other1.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.777
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg11.655
r_dihedral_angle_1_deg5.844
r_long_range_B_refined5.338
r_long_range_B_other5.031
r_angle_refined_deg1.481
r_scangle_other1.41
r_mcangle_it1.128
r_mcangle_other1.128
r_angle_other_deg0.945
r_scbond_it0.86
r_scbond_other0.86
r_mcbond_it0.671
r_mcbond_other0.67
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms9893
Nucleic Acid Atoms
Solvent Atoms1381
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing