6E85

1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-4-phosphate Dehydrogenase from Klebsiella pneumoniae.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HI1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5292Protein: 6.9 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.355α = 90
b = 76.216β = 106.78
c = 92.113γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.253099.80.0530.0530.060.02824.64.3177342-312.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.2797.70.5490.5490.6540.3490.82.33.3

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 REPLACEMENTTHROUGHOUT2HI11.2529.67168266894199.770.115090.113840.1392RANDOM16.874
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]
0.330.010.24-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.359
r_sphericity_free19.899
r_dihedral_angle_4_deg13.475
r_dihedral_angle_3_deg11.275
r_rigid_bond_restr8.784
r_sphericity_bonded6.937
r_dihedral_angle_1_deg4.679
r_long_range_B_refined3.057
r_long_range_B_other2.545
r_scangle_other1.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.359
r_sphericity_free19.899
r_dihedral_angle_4_deg13.475
r_dihedral_angle_3_deg11.275
r_rigid_bond_restr8.784
r_sphericity_bonded6.937
r_dihedral_angle_1_deg4.679
r_long_range_B_refined3.057
r_long_range_B_other2.545
r_scangle_other1.981
r_scbond_it1.685
r_scbond_other1.613
r_mcangle_it1.458
r_mcangle_other1.457
r_angle_refined_deg1.283
r_mcbond_it1.261
r_mcbond_other1.261
r_angle_other_deg0.489
r_chiral_restr0.071
r_gen_planes_refined0.042
r_gen_planes_other0.04
r_bond_refined_d0.006
r_bond_other_d0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4923
Nucleic Acid Atoms
Solvent Atoms954
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing