☰ Navigation Tabs
Crystal Structure of FIV Capsid C-Terminal Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 0.056M Sodium phosphate monobasic monohydrate, 1.344M Pottasium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.19 α = 90 b = 64.19 β = 90 c = 178.56 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2014-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.29 40.63 99.71 0.108 17.91 16.3 10456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.372 96.96 0.529 2.92 6.4
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 3DTJ 2.29 40.63 9946 504 99.61 0.23777 0.23529 0.24 0.28683 0.2875 RANDOM 41.833
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] -17.21 -17.21 34.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.104 r_dihedral_angle_4_deg 17.135 r_dihedral_angle_3_deg 14.936 r_long_range_B_refined 10.006 r_long_range_B_other 9.981 r_dihedral_angle_1_deg 6.708 r_scangle_other 6.019 r_mcangle_it 6.001 r_mcangle_other 5.997 r_scbond_it 3.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.104 r_dihedral_angle_4_deg 17.135 r_dihedral_angle_3_deg 14.936 r_long_range_B_refined 10.006 r_long_range_B_other 9.981 r_dihedral_angle_1_deg 6.708 r_scangle_other 6.019 r_mcangle_it 6.001 r_mcangle_other 5.997 r_scbond_it 3.981 r_scbond_other 3.962 r_mcbond_it 3.872 r_mcbond_other 3.844 r_angle_refined_deg 1.515 r_angle_other_deg 1.061 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 1141 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing