6H3D

Staphylopine dehydrogenase in complex with xNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GMZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M ammonium acetate, 22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.09α = 90
b = 48.75β = 90
c = 59.4γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0592.5499.22.34.1142598
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1

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 REPLACEMENTTHROUGHOUT6GMZ2.0592.5432581173399.20.193440.191620.22852RANDOM54.126
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]
-0.73-2.863.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.187
r_dihedral_angle_3_deg18.663
r_dihedral_angle_4_deg18.347
r_long_range_B_other12.016
r_long_range_B_refined12.014
r_scangle_other10.065
r_dihedral_angle_1_deg7.497
r_scbond_it6.92
r_scbond_other6.919
r_mcangle_other6.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.187
r_dihedral_angle_3_deg18.663
r_dihedral_angle_4_deg18.347
r_long_range_B_other12.016
r_long_range_B_refined12.014
r_scangle_other10.065
r_dihedral_angle_1_deg7.497
r_scbond_it6.92
r_scbond_other6.919
r_mcangle_other6.318
r_mcangle_it6.315
r_mcbond_it5.018
r_mcbond_other5.01
r_angle_refined_deg2.225
r_angle_other_deg1.152
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.01
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 Atoms3476
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing