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Crystal structure of EV71 3C Proteinase in complex with Compound VIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GHQ PDB ENTRY 4GHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 100MM TRIS, 25% PEG4000, 0.8M LITHIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 1.86 33.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.948 α = 90 b = 64.084 β = 91.11 c = 76.489 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2012-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.86 50 96 0.0407 9.9 2.28 25588
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 1.86 1.92 86.6 0.2694 1.9 2.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 4GHQ 1.86 45.65 25588 1283 96 0.197 0.196 0.1955 0.225 0.2249 RANDOM 22.28
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] 0.56 -0.53 -0.87 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.776 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_1_deg 6.167 r_angle_refined_deg 1.752 r_angle_other_deg 1.503 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.776 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_1_deg 6.167 r_angle_refined_deg 1.752 r_angle_other_deg 1.503 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other 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 243 Heterogen Atoms 64
Software Software Software Name Purpose AUTOMAR data reduction AUTOMAR data scaling PHASER phasing REFMAC refinement