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Atomic-resolution crystal structure of the Recombinant form of Scytovirin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QT4 PDB ENTRY 2QT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1M sodium citrate, 0.1 M imidazole pH 8.0, protein concentration 32 MG/ML
VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.2 α = 90 b = 38.79 β = 90 c = 59.87 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD 2007-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.979 APS 22-ID
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 1 50 98.8 0.057 19.3 4.6 48601 48018 -3
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 1 1.02 85.3 0.404 1.9 2.2 2030
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 SAD/DIRECT REFINEMENT THROUGHOUT PDB ENTRY 2QT4 1 30 47944 980 98.56 0.129 0.128 0.1378 0.147 0.1581 RANDOM 10.18
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] 0.24 -0.12 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_sphericity_free 12.036 r_dihedral_angle_3_deg 10.879 r_dihedral_angle_4_deg 6.269 r_dihedral_angle_1_deg 5.854 r_sphericity_bonded 4.858 r_scangle_it 3.687 r_scbond_it 3.501 r_mcangle_it 3.178 r_mcbond_it 2.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_sphericity_free 12.036 r_dihedral_angle_3_deg 10.879 r_dihedral_angle_4_deg 6.269 r_dihedral_angle_1_deg 5.854 r_sphericity_bonded 4.858 r_scangle_it 3.687 r_scbond_it 3.501 r_mcangle_it 3.178 r_mcbond_it 2.565 r_rigid_bond_restr 1.584 r_angle_refined_deg 1.392 r_mcbond_other 1.203 r_angle_other_deg 0.885 r_xyhbond_nbd_refined 0.26 r_symmetry_vdw_other 0.255 r_nbd_other 0.204 r_nbd_refined 0.196 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.132 r_nbtor_other 0.089 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 674 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SHELXS phasing