☰ Navigation Tabs
Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris-HCl pH 8.5, 35% PEG 4000, 0.4M LiSO4, 0.4M Guanidine-HCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.703 α = 93.06 b = 69.262 β = 95.03 c = 191.388 γ = 97.56
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 4 mirrors 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9792 NSLS X8C
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 2.21 182.57 97.5 0.082 20.7 3.9 103935 103935 2 2
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) 2.21 2.29 91.5 0.28 4.5 3.4 9718
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.21 182.57 103935 103863 5185 98.27 0.2 0.194 0.19 0.1886 0.267 0.2631 RANDOM 24.932
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] -0.08 -0.86 -0.65 1.66 -0.26 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.474 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 17.978 r_dihedral_angle_1_deg 6.92 r_scangle_it 3.968 r_scbond_it 2.675 r_angle_refined_deg 1.754 r_mcangle_it 1.591 r_mcbond_it 1.083 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.474 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 17.978 r_dihedral_angle_1_deg 6.92 r_scangle_it 3.968 r_scbond_it 2.675 r_angle_refined_deg 1.754 r_mcangle_it 1.591 r_mcbond_it 1.083 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15142 Nucleic Acid Atoms Solvent Atoms 1216 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing