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JC Polyomavirus VP1 five-fold pore mutant P223M
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 57.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.72 α = 90 b = 95.63 β = 110.4 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 2.1 50 99.8 9.2 3.8 98969 29.8
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 2.1 2.15 99.8 1.7 3.7
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 2.1 50 94028 4940 99.83 0.18195 0.18008 0.187 0.21775 0.2226 RANDOM 28.892
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] 0.49 0.2 -0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.444 r_long_range_B_refined 6.202 r_long_range_B_other 6.202 r_scangle_other 4.501 r_scbond_it 3.237 r_scbond_other 3.231 r_mcangle_it 2.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.444 r_long_range_B_refined 6.202 r_long_range_B_other 6.202 r_scangle_other 4.501 r_scbond_it 3.237 r_scbond_other 3.231 r_mcangle_it 2.289 r_mcangle_other 2.289 r_mcbond_it 1.697 r_mcbond_other 1.697 r_angle_refined_deg 1.307 r_angle_other_deg 0.734 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 10031 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building XSCALE data scaling PHASER phasing