4XB1

Hyperthermophilic archaeal homoserine dehydrogenase in complex with NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DO5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22932-methyl-2,4-pentandiol, potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
4.3571.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.56α = 90
b = 112.56β = 90
c = 95.885γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702012-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.35099.80.05121.47.653097
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3899.90.2859.17.5

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 REPLACEMENTTHROUGHOUT3DO52.35050089268599.190.17050.16870.2046RANDOM46.494
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]
0.350.35-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.403
r_dihedral_angle_4_deg20.562
r_dihedral_angle_3_deg18.106
r_dihedral_angle_1_deg6.843
r_mcangle_it5.721
r_mcbond_it4.166
r_mcbond_other4.165
r_angle_refined_deg2.133
r_angle_other_deg0.956
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.403
r_dihedral_angle_4_deg20.562
r_dihedral_angle_3_deg18.106
r_dihedral_angle_1_deg6.843
r_mcangle_it5.721
r_mcbond_it4.166
r_mcbond_other4.165
r_angle_refined_deg2.133
r_angle_other_deg0.956
r_chiral_restr0.135
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4916
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms138

Software

Software
Software NamePurpose
HKL-2000data reduction
DMrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing