☰ Navigation Tabs
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in apo form
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 Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEG-4000) and equilibrated against the precipitant solution.
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.896 α = 86.58 b = 41.283 β = 89.67 c = 59.118 γ = 75.06
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 EIGER2 XE 9M 2023-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97949 NSLS-II 19-ID
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 1.65 59.01 88.7 0.037 12.8 1.8 32373
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 1.65 1.73 51 0.078 9.85
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 1.65 59.01 32373 1631 88.79 0.14773 0.14595 0.1469 0.18336 0.1829 RANDOM 16.04
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] -0.29 -0.33 0.33 0.53 -0.18 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.989 r_dihedral_angle_2_deg 8.54 r_long_range_B_refined 6.254 r_long_range_B_other 6.168 r_dihedral_angle_1_deg 5.891 r_scangle_other 4.662 r_scbond_it 2.961 r_scbond_other 2.96 r_mcangle_it 2.857 r_mcangle_other 2.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.989 r_dihedral_angle_2_deg 8.54 r_long_range_B_refined 6.254 r_long_range_B_other 6.168 r_dihedral_angle_1_deg 5.891 r_scangle_other 4.662 r_scbond_it 2.961 r_scbond_other 2.96 r_mcangle_it 2.857 r_mcangle_other 2.856 r_mcbond_it 1.857 r_mcbond_other 1.854 r_angle_refined_deg 1.581 r_angle_other_deg 0.541 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 2802 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing