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HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with 2-((2,4-difluorobenzyl)amino)-2-oxoacetic acid
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 298 Protein-compound mixture in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA, 5% DMSO were mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the precipitant solution.
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.536 α = 78.07 b = 44.328 β = 89.99 c = 59.863 γ = 81.69
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 2022-02-07 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 1.7 38.69 89.4 0.049 8.8 2 34755
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 1.7 1.73 80.9 0.229 2.7 1.9
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 1.7 38.69 32683 2065 89.31 0.1786 0.17587 0.1906 0.22265 0.2356 RANDOM 29.235
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] 0.75 -1.78 0.41 1.04 -0.55 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.507 r_dihedral_angle_2_deg 7.042 r_long_range_B_refined 6.891 r_long_range_B_other 6.859 r_dihedral_angle_1_deg 5.802 r_scangle_other 5.327 r_mcangle_it 3.981 r_mcangle_other 3.981 r_scbond_it 3.522 r_scbond_other 3.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.507 r_dihedral_angle_2_deg 7.042 r_long_range_B_refined 6.891 r_long_range_B_other 6.859 r_dihedral_angle_1_deg 5.802 r_scangle_other 5.327 r_mcangle_it 3.981 r_mcangle_other 3.981 r_scbond_it 3.522 r_scbond_other 3.521 r_mcbond_it 2.771 r_mcbond_other 2.761 r_angle_refined_deg 1.43 r_angle_other_deg 0.486 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 2804 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing