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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 2P4D PDB ENTRY 2P4D Variola major H1 phosphatase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH 7 294.15 82% PEG 400, 0.1M MOPS pH 7.0, BATCH, temperature 294.15K
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.638 α = 90 b = 63.994 β = 90 c = 135.428 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 Xcalibur 2007-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 6 85.9 0.054 0.054 22.4 6.6 10692 10692 1 1 16.031
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 65.2 0.169 0.169 9.4 3.1 1148
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2P4D
Variola major H1 phosphatase 1.95 6 12159 10161 511 87.77 0.18794 0.18691 0.20813 RANDOM 20.843
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] -0.02 0.16 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 24.188 r_dihedral_angle_3_deg 22.102 r_scangle_it 6.096 r_dihedral_angle_1_deg 5.904 r_scbond_it 4.429 r_mcangle_it 3.404 r_mcbond_it 2.348 r_angle_refined_deg 1.46 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 24.188 r_dihedral_angle_3_deg 22.102 r_scangle_it 6.096 r_dihedral_angle_1_deg 5.904 r_scbond_it 4.429 r_mcangle_it 3.404 r_mcbond_it 2.348 r_angle_refined_deg 1.46 r_nbtor_refined 0.332 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.227 r_symmetry_hbond_refined 0.183 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1374 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection MOSFLM data reduction SCALA data scaling MOLREP phasing