2HW4

Crystal structure of human phosphohistidine phosphatase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSe-Met MAD structure determined from other crystals

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52981.9 M Sodium Formate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.53α = 90
b = 112.53β = 90
c = 29.37γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.033130ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.93097.50.05620.625.61066510665-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9288.80.2266.474.8

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 REPLACEMENTTHROUGHOUTSe-Met MAD structure determined from other crystals1.921.27101511015151097.520.1790.173250.17070.22469RANDOM24.399
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.756
r_dihedral_angle_4_deg23.97
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg7.258
r_scangle_it4.285
r_scbond_it3.21
r_mcangle_it2.153
r_mcbond_it1.801
r_angle_refined_deg1.774
r_angle_other_deg1.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.756
r_dihedral_angle_4_deg23.97
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg7.258
r_scangle_it4.285
r_scbond_it3.21
r_mcangle_it2.153
r_mcbond_it1.801
r_angle_refined_deg1.774
r_angle_other_deg1.092
r_mcbond_other0.354
r_symmetry_vdw_other0.265
r_symmetry_hbond_refined0.258
r_nbd_refined0.207
r_xyhbond_nbd_refined0.206
r_nbd_other0.2
r_nbtor_refined0.186
r_symmetry_vdw_refined0.144
r_chiral_restr0.122
r_nbtor_other0.088
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms985
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing