4E5N

Thermostable phosphite dehydrogenase in complex with NAD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528525-30% PEG 3350, 100 mM KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthew coefficientSolvent content
2.2946.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.71α = 90
b = 113.54β = 100.16
c = 130.19γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-DAPS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.780950.05419.26270433
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.874.10.43633.844707

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 REPLACEMENTTHROUGHOUTThermostable phosphite dehydrogenase E175A variant1.725256745136231000.2120.210160.24698RANDOM29.973
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]
0.44-0.23-1.330.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.545
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg5.371
r_scangle_it2.293
r_scbond_it1.374
r_angle_refined_deg1.159
r_mcangle_it0.918
r_mcbond_it0.481
r_angle_other_deg0.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.545
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg5.371
r_scangle_it2.293
r_scbond_it1.374
r_angle_refined_deg1.159
r_mcangle_it0.918
r_mcbond_it0.481
r_angle_other_deg0.252
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20133
Nucleic Acid Atoms
Solvent Atoms2458
Heterogen Atoms352

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling