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Crystal structure of human phosphohistidine phosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Se-Met MAD structure determined from other crystals
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.9 M Sodium Formate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.53 α = 90 b = 112.53 β = 90 c = 29.37 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2006-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.033130 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 30 97.5 0.056 20.62 5.6 10665 10665 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 88.8 0.226 6.47 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Se-Met MAD structure determined from other crystals 1.9 21.27 10151 10151 510 97.52 0.179 0.17325 0.1707 0.1773 0.22469 0.2313 RANDOM 24.399
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 23.97 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 7.258 r_scangle_it 4.285 r_scbond_it 3.21 r_mcangle_it 2.153 r_mcbond_it 1.801 r_angle_refined_deg 1.774 r_angle_other_deg 1.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 23.97 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 7.258 r_scangle_it 4.285 r_scbond_it 3.21 r_mcangle_it 2.153 r_mcbond_it 1.801 r_angle_refined_deg 1.774 r_angle_other_deg 1.092 r_mcbond_other 0.354 r_symmetry_vdw_other 0.265 r_symmetry_hbond_refined 0.258 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.206 r_nbd_other 0.2 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.122 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 985 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHARP phasing