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High Resolution Crystal Structure of the Vaccinia Virus Dual-Specificity Phosphatase VH1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RF6 PDB Entry 2RF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Batch 8 297 62% PEG 400, 0.1M Tris pH 8 , Batch, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.816 α = 90 b = 38.69 β = 90 c = 134.987 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC Q-270 Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block. Rh-coated Si mirror for vertical focusing. 2007-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.918 CHESS F1
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 1.32 20 90.9 0.057 65.6 15.7 39499 35905 19.326
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) 1.32 1.37 51.4 0.357 2.5 4.4 3868
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 PDB Entry 2RF6 1.32 14.11 37455 33998 1800 90.77 0.1717 0.1717 0.17098 0.167 0.18458 0.1789 RANDOM 26.352
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.513 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_3_deg 15.109 r_scangle_it 6.064 r_dihedral_angle_1_deg 5.494 r_mcangle_it 3.819 r_scbond_it 3.739 r_mcbond_it 2.158 r_angle_refined_deg 1.186 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.513 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_3_deg 15.109 r_scangle_it 6.064 r_dihedral_angle_1_deg 5.494 r_mcangle_it 3.819 r_scbond_it 3.739 r_mcbond_it 2.158 r_angle_refined_deg 1.186 r_nbtor_refined 0.32 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.242 r_symmetry_hbond_refined 0.229 r_symmetry_vdw_refined 0.207 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1366 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing