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JC Polyomavirus VP1 five-fold pore mutant N221W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.34 α = 90 b = 95.98 β = 110.48 c = 128.51 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2010-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 98.8 11.7 4.1 155280 30.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 88.5 1.5
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 3NXG 1.8 50 147490 7790 98.82 0.16109 0.15979 0.1699 0.18584 0.1946 RANDOM 26.921
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] 0.16 -0.03 0.51 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.097 r_dihedral_angle_4_deg 14.922 r_dihedral_angle_3_deg 11.973 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 6.314 r_long_range_B_other 6.314 r_scangle_other 4.162 r_scbond_other 3.08 r_scbond_it 3.079 r_mcangle_it 2.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.097 r_dihedral_angle_4_deg 14.922 r_dihedral_angle_3_deg 11.973 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 6.314 r_long_range_B_other 6.314 r_scangle_other 4.162 r_scbond_other 3.08 r_scbond_it 3.079 r_mcangle_it 2.193 r_mcangle_other 2.193 r_mcbond_it 1.706 r_mcbond_other 1.705 r_angle_refined_deg 1.269 r_angle_other_deg 0.729 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 10033 Nucleic Acid Atoms Solvent Atoms 873 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction XSCALE data scaling PHASER phasing