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HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with HEPES
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 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the precipitant solution (100 mM HEPES pH7.5, 50 mM NH4F, 28% (w/v) PEG 4K) and equilibrated against the precipitant solution.
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.42 α = 90 b = 59.25 β = 98.21 c = 60.286 γ = 90
Symmetry Space Group P 1 21 1
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 2022-11-07 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 1.9 38.2 98.1 0.041 17.7 3.5 27321
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 1.9 1.94 87.6 0.157 2.6
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 1.9 38.2 25672 1631 97.92 0.1496 0.14695 0.1615 0.19124 0.1986 RANDOM 19.955
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] 1.15 -1.34 -0.34 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.085 r_dihedral_angle_3_deg 13.819 r_long_range_B_refined 6.593 r_long_range_B_other 6.529 r_dihedral_angle_1_deg 5.875 r_scangle_other 5.214 r_scbond_it 3.278 r_scbond_other 3.277 r_mcangle_it 3.059 r_mcangle_other 3.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.085 r_dihedral_angle_3_deg 13.819 r_long_range_B_refined 6.593 r_long_range_B_other 6.529 r_dihedral_angle_1_deg 5.875 r_scangle_other 5.214 r_scbond_it 3.278 r_scbond_other 3.277 r_mcangle_it 3.059 r_mcangle_other 3.058 r_mcbond_it 2.045 r_mcbond_other 2.03 r_angle_refined_deg 1.475 r_angle_other_deg 0.476 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 2822 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing