4PG6

Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.0


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2M Magnesium acetate, 16% PEG3350, 0.1M HEPES, pH7.0, 5%Glycerol, 20% Iso-propanol
Crystal Properties
Matthews coefficientSolvent content
2.4549.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.64α = 90
b = 116.88β = 90
c = 118.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97625ESRFBM14

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
12.2118.6210017.38.35205047.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321000.4420.4420.1621.78.47494

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 REPLACEMENTTHROUGHOUT3DO52.234.74933026511000.2050.2030.244RANDOM34.58
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]
-1.322.08-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.906
r_dihedral_angle_3_deg14.399
r_long_range_B_refined6.462
r_long_range_B_other6.462
r_dihedral_angle_1_deg6.272
r_scangle_other3.85
r_mcangle_other3.588
r_mcangle_it3.587
r_scbond_it2.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.906
r_dihedral_angle_3_deg14.399
r_long_range_B_refined6.462
r_long_range_B_other6.462
r_dihedral_angle_1_deg6.272
r_scangle_other3.85
r_mcangle_other3.588
r_mcangle_it3.587
r_scbond_it2.422
r_scbond_other2.422
r_mcbond_it2.249
r_mcbond_other2.235
r_angle_refined_deg1.338
r_angle_other_deg0.964
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms5787
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
MOSFLMdata reduction