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Ryegrass mottle virus serine protease domain fused with VPg 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 9 293 0.1 M MIB, pH 9.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.94 α = 90 b = 67.52 β = 90 c = 74.08 γ = 90
Symmetry Space Group P 21 21 21
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 2016-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.96411 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 2.1 74.08 99.8 0.077 0.084 0.034 0.998 13.9 5.8 11945
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 2.1 2.21 99.8 0.38 0.417 0.17 0.924 4.2 5.9
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 2.1 49.9 11317 591 99.73 0.17623 0.17319 0.1849 0.23481 0.2372 RANDOM 31.683
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] 1.82 0.26 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.45 r_dihedral_angle_4_deg 20.773 r_dihedral_angle_3_deg 16.832 r_long_range_B_refined 7.372 r_long_range_B_other 7.337 r_dihedral_angle_1_deg 6.853 r_scangle_other 5.689 r_mcangle_other 4.009 r_mcangle_it 4.006 r_scbond_it 3.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.45 r_dihedral_angle_4_deg 20.773 r_dihedral_angle_3_deg 16.832 r_long_range_B_refined 7.372 r_long_range_B_other 7.337 r_dihedral_angle_1_deg 6.853 r_scangle_other 5.689 r_mcangle_other 4.009 r_mcangle_it 4.006 r_scbond_it 3.837 r_scbond_other 3.82 r_angle_other_deg 3.803 r_mcbond_it 2.882 r_mcbond_other 2.87 r_angle_refined_deg 1.897 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_other 0.016 r_gen_planes_refined 0.01 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 1433 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing