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Ryegrass mottle virus protease domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES 7.5, 22.5% PEG 3350, 0.22M LiSO4, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.11 α = 90 b = 115.99 β = 105.27 c = 57.92 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS PILATUS 6M 2017-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 57.99 95.98 0.123 0.149 0.083 0.989 5.3 3 19160 45.496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 98.69 0.548 0.662 0.365 0.644 2.1 3.1
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 1ZYO 2.3 57.99 19160 1002 95.98 0.23229 0.22946 0.2349 0.29018 0.2893 RANDOM 45.366
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] -1.79 -0.03 -3.06 4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.678 r_dihedral_angle_4_deg 21.571 r_dihedral_angle_3_deg 20.435 r_long_range_B_other 8.737 r_long_range_B_refined 8.735 r_dihedral_angle_1_deg 7.685 r_mcangle_it 5.707 r_mcangle_other 5.706 r_scangle_other 5.241 r_angle_other_deg 3.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.678 r_dihedral_angle_4_deg 21.571 r_dihedral_angle_3_deg 20.435 r_long_range_B_other 8.737 r_long_range_B_refined 8.735 r_dihedral_angle_1_deg 7.685 r_mcangle_it 5.707 r_mcangle_other 5.706 r_scangle_other 5.241 r_angle_other_deg 3.878 r_mcbond_it 3.508 r_mcbond_other 3.508 r_scbond_other 3.287 r_scbond_it 3.285 r_angle_refined_deg 1.767 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing