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L54F Variant of JC Polyomavirus Major Capsid Protein VP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG PDB entry 3NXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 0.2 M KSCN, 12% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.43 α = 90 b = 95.71 β = 110.27 c = 128.8 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 PIXEL DECTRIS PILATUS 2M-F 2012-03-15 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 1.9 47 99.3 15.14 4.2 132607 132607 -3 -3 26
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 1.9 1.95 96.9 2.55 3.9 9546
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 3NXG 1.9 44.53 132607 125934 6673 99.35 0.15093 0.14917 0.1583 0.18487 0.1917 RANDOM 20.481
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.415 r_angle_other_deg 0.774 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.415 r_angle_other_deg 0.774 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 9967 Nucleic Acid Atoms Solvent Atoms 1161 Heterogen Atoms 68
Software Software Software Name Purpose REMAQ data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling