X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829316% PAA, 20mM MgCl2, 0.1 m Tris pH8, 4mM NAD+, 10mM Acetophenone, 7 mg/ml ADH-A
Crystal Properties
Matthews coefficientSolvent content
2.4950.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.689α = 90
b = 109.458β = 90
c = 256.653γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.2129.74990.1680.0920.9957.87.414434825.9
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)
12.212.2580.90.680.2850.7632.45.9

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 REPLACEMENTTHROUGHOUT3jv72.2229.64136802730699.260.194630.193510.21576RANDOM39.583
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]
2.130.39-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.723
r_dihedral_angle_4_deg18.857
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg5.659
r_long_range_B_refined3.416
r_long_range_B_other3.373
r_angle_refined_deg1.426
r_scangle_other1.164
r_mcangle_it1.13
r_mcangle_other1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.723
r_dihedral_angle_4_deg18.857
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg5.659
r_long_range_B_refined3.416
r_long_range_B_other3.373
r_angle_refined_deg1.426
r_scangle_other1.164
r_mcangle_it1.13
r_mcangle_other1.13
r_angle_other_deg0.945
r_scbond_it0.682
r_scbond_other0.682
r_mcbond_it0.64
r_mcbond_other0.64
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms19705
Nucleic Acid Atoms
Solvent Atoms752
Heterogen Atoms368

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing