2P69

Crystal Structure of Human Pyridoxal Phosphate Phosphatase with PLP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52980.1 M Citric acid pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.559α = 90
b = 54.559β = 90
c = 212.537γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE 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)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
12.255099.80.097.4131616316163
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)
12.252.3399.80.82512.61569

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2YOC2.2536.27160861608680599.730.210.2080.25RANDOM52.817
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]
0.110.11-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_4_deg15.625
r_dihedral_angle_3_deg15.575
r_scangle_it8.879
r_scbond_it6.56
r_dihedral_angle_1_deg5.854
r_mcangle_it3.838
r_mcbond_it2.712
r_angle_refined_deg1.361
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_4_deg15.625
r_dihedral_angle_3_deg15.575
r_scangle_it8.879
r_scbond_it6.56
r_dihedral_angle_1_deg5.854
r_mcangle_it3.838
r_mcbond_it2.712
r_angle_refined_deg1.361
r_nbtor_refined0.313
r_nbd_refined0.202
r_xyhbond_nbd_refined0.187
r_symmetry_vdw_refined0.129
r_symmetry_hbond_refined0.124
r_metal_ion_refined0.12
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2175
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms17

Software

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