3LY1

Crystal structure of Putative histidinol-phosphate aminotransferase (YP_050345.1) from Erwinia carotovora atroseptica SCRI1043 at 1.80 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627720.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.856.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.625α = 90
b = 150.477β = 94.38
c = 100.092γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-11-07MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.96109,0.97946,0.97936SSRLBL9-2

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
11.829.56496.50.0598.36158547-323.011
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)
11.791.8579.80.6751.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.829.564158407795299.320.1780.1760.206RANDOM17.717
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]
0.66-1.05-3.332.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.055
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg6.053
r_scangle_it3.463
r_scbond_it2.228
r_angle_refined_deg1.533
r_mcangle_it1.268
r_angle_other_deg0.946
r_mcbond_it0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.055
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg6.053
r_scangle_it3.463
r_scbond_it2.228
r_angle_refined_deg1.533
r_mcangle_it1.268
r_angle_other_deg0.946
r_mcbond_it0.772
r_mcbond_other0.254
r_chiral_restr0.089
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10683
Nucleic Acid Atoms
Solvent Atoms1792
Heterogen Atoms208

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
MolProbitymodel building