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Crystal structure of the C-terminal domain from the Rous Sarcoma Virus capsid protein: mutant D179A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G28 PDB ENTRY 3G28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 291 0.2M Succinic acid/KOH, pH4.3, 24% PEG8000, 1M Sodium Nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.763 α = 90 b = 76.708 β = 90 c = 32.515 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate Rigaku Varimax HF confocal optics 2008-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 38 100 0.078 9.2 10.7 6413 6413
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) 2 2.07 100 0.333 2.8 10.5 630
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3G28 2 38 6086 6086 317 99.74 0.19815 0.19815 0.19655 0.22842 0.2211 RANDOM 21.479
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 0.85 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_4_deg 24.112 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_1_deg 4.556 r_scangle_it 3.231 r_scbond_it 1.997 r_angle_refined_deg 1.368 r_mcangle_it 1.342 r_mcbond_it 0.723 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_4_deg 24.112 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_1_deg 4.556 r_scangle_it 3.231 r_scbond_it 1.997 r_angle_refined_deg 1.368 r_mcangle_it 1.342 r_mcbond_it 0.723 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 601 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling