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Crystal structure of mavirus major capsid protein lacking the C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.1 M tri-sodium citrate, 1.2 - 1.7 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.19 α = 90 b = 132.58 β = 90 c = 135.22 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 100 PIXEL DECTRIS PILATUS 6M 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.979 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 47.33 99.6 0.077 0.085 0.996 12.89 5.575 372727 23.515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 99.7 0.41 0.452 0.891 3.95 5.55
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 6G43 1.5 47.33 354090 18637 99.64 0.1658 0.1649 0.165 0.1829 0.1827 RANDOM 17.596
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] 0.3 0.05 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.508 r_dihedral_angle_3_deg 10.807 r_dihedral_angle_4_deg 8.481 r_dihedral_angle_1_deg 6.163 r_angle_refined_deg 1.508 r_angle_other_deg 0.918 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.508 r_dihedral_angle_3_deg 10.807 r_dihedral_angle_4_deg 8.481 r_dihedral_angle_1_deg 6.163 r_angle_refined_deg 1.508 r_angle_other_deg 0.918 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11840 Nucleic Acid Atoms Solvent Atoms 1693 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing