2X4D

Crystal structure of human phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HLTPDB ENTRY 3HLT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.3M NA FORMATE, 25W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.21α = 90
b = 39.41β = 91.79
c = 112.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.9231.6294.40.099.34.1378471.7
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)
11.922.0368.10.41.72.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3HLT1.924035942190294.20.2290.2270.250.258RANDOM7.93
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]
-0.970.831.72-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.605
r_dihedral_angle_4_deg22.261
r_dihedral_angle_3_deg14.59
r_dihedral_angle_1_deg6.071
r_scangle_it2.761
r_scbond_it1.963
r_angle_other_deg1.727
r_angle_refined_deg1.558
r_mcangle_it0.984
r_mcbond_it0.613
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3455
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing