2P27

Crystal Structure of Human Pyridoxal Phosphate Phosphatase with Mg2+ at 1.9 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YOCPDB entry 2YOC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298100mM Tris-HCl pH 8.5, 17% PEG 20000, 100mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3647.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.245α = 90
b = 54.245β = 90
c = 213.182γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97900NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9501000.0680.0529.58.32627426274
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)
1.91.971000.6248.24819

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2YOC1.948.342618226182133299.980.2130.2130.2110.25RANDOM32.203
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]
0.290.29-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg17.508
r_dihedral_angle_3_deg15.049
r_dihedral_angle_1_deg7.347
r_scangle_it3.453
r_scbond_it2.199
r_mcangle_it1.538
r_angle_refined_deg1.454
r_mcbond_it0.906
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg17.508
r_dihedral_angle_3_deg15.049
r_dihedral_angle_1_deg7.347
r_scangle_it3.453
r_scbond_it2.199
r_mcangle_it1.538
r_angle_refined_deg1.454
r_mcbond_it0.906
r_nbtor_refined0.3
r_nbd_refined0.203
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.143
r_symmetry_vdw_refined0.13
r_chiral_restr0.088
r_metal_ion_refined0.022
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2236
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing