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Crystal Structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P6122
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1M Tris-HCl pH 8.5, 22% PEG 2000 MME, 0.45M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.953 α = 90 b = 76.953 β = 90 c = 136.347 γ = 120
Symmetry Space Group P 61 2 2
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) 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 2.3 47.7 99.9 0.076 0.076 23.5 11.5 11248 11248 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) 1 2.3 2.42 99.8 0.186 9.8 11.9 1584
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 SAD THROUGHOUT 2.3 25.52 11248 11186 538 99.84 0.2 0.184 0.182 0.1809 0.235 0.2323 RANDOM 23.945
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 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.848 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 5.954 r_dihedral_angle_4_deg 5.175 r_scangle_it 2.91 r_scbond_it 2.001 r_angle_refined_deg 1.476 r_mcangle_it 1.434 r_mcbond_it 0.924 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.848 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 5.954 r_dihedral_angle_4_deg 5.175 r_scangle_it 2.91 r_scbond_it 2.001 r_angle_refined_deg 1.476 r_mcangle_it 1.434 r_mcbond_it 0.924 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.22 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1337 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing