3MBH

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720.00% polyethylene glycol 3000, 0.20M sodium chloride, 0.1M HEPES pH 7.5, Additive: 0.001 M pyridoxal, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3246.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.723α = 90
b = 138.368β = 90
c = 143.539γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
1229.81498.30.04812.12125843-330.527
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)
122.0797.50.5541.5

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 DIFFRACTIONSADTHROUGHOUT229.814125765630699.570.1690.1670.206RANDOM21.723
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]
-0.630.190.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.022
r_dihedral_angle_4_deg20.251
r_dihedral_angle_3_deg13.841
r_dihedral_angle_1_deg5.943
r_scangle_it3.611
r_scbond_it2.412
r_angle_refined_deg1.622
r_mcangle_it1.397
r_angle_other_deg0.977
r_mcbond_it0.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.022
r_dihedral_angle_4_deg20.251
r_dihedral_angle_3_deg13.841
r_dihedral_angle_1_deg5.943
r_scangle_it3.611
r_scbond_it2.412
r_angle_refined_deg1.622
r_mcangle_it1.397
r_angle_other_deg0.977
r_mcbond_it0.793
r_mcbond_other0.262
r_chiral_restr0.098
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13632
Nucleic Acid Atoms
Solvent Atoms1022
Heterogen Atoms76

Software

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