6A0U | pdb_00006a0u

Homoserine dehydrogenase K195A mutant from Thermus thermophilus HB8 complexed with HSE and NADP+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XDF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Sodium formate, CAPS pH 10.0
Crystal Properties
Matthews coefficientSolvent content
4.270.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.675α = 90
b = 119.675β = 90
c = 143.714γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102014-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.935099.90.10149.88.489383
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)
11.931.961000.3637.58.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5XDF1.935084852447599.90.1740.1720.180.2120.22RANDOM30.99
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]
-0.3-0.15-0.30.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.883
r_dihedral_angle_4_deg22.034
r_dihedral_angle_3_deg13.051
r_long_range_B_refined8.616
r_long_range_B_other8.616
r_dihedral_angle_1_deg7.337
r_scangle_other6.344
r_mcangle_other4.471
r_mcangle_it4.47
r_scbond_other4.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.883
r_dihedral_angle_4_deg22.034
r_dihedral_angle_3_deg13.051
r_long_range_B_refined8.616
r_long_range_B_other8.616
r_dihedral_angle_1_deg7.337
r_scangle_other6.344
r_mcangle_other4.471
r_mcangle_it4.47
r_scbond_other4.408
r_scbond_it4.407
r_angle_other_deg3.707
r_mcbond_it3.487
r_mcbond_other3.486
r_angle_refined_deg2.437
r_chiral_restr0.163
r_bond_refined_d0.027
r_gen_planes_other0.023
r_gen_planes_refined0.014
r_bond_other_d
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 Atoms4973
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms198

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing