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HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 protein in 50 mM Tris-Cl, pH 8.0, 1 mM TCEP was mixed with the precipitation buffer (0.1M Sodium potassium phosphate pH 7.0, 28% w/v Polyethylene glycol 3,350) and equilibrated against it
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.086 α = 90 b = 54.703 β = 90 c = 100.833 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 37.1 96.9 0.101 13.6 6.7 17592
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 98 0.791 3.1 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 37.1 16712 843 96.51 0.15628 0.15454 0.1686 0.19098 0.2039 RANDOM 17.552
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] -0.11 0.78 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.113 r_long_range_B_refined 7.423 r_long_range_B_other 7.212 r_dihedral_angle_2_deg 6.545 r_dihedral_angle_1_deg 5.646 r_scangle_other 5.501 r_scbond_other 3.54 r_scbond_it 3.538 r_mcangle_other 3.184 r_mcangle_it 3.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.113 r_long_range_B_refined 7.423 r_long_range_B_other 7.212 r_dihedral_angle_2_deg 6.545 r_dihedral_angle_1_deg 5.646 r_scangle_other 5.501 r_scbond_other 3.54 r_scbond_it 3.538 r_mcangle_other 3.184 r_mcangle_it 3.178 r_mcbond_it 2.036 r_mcbond_other 1.965 r_angle_refined_deg 1.539 r_angle_other_deg 0.535 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1391 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing