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Crystal Structure of SH3-like_bac-type domain (79-145) of Conserved domain protein GBAA_2967 from Bacillus anthracis Ames ancestor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A6L7HMQ8-F1 UniProt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 6.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3;
Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG3350;
Cryo: Reservoir
Crystal Properties Matthews coefficient Solvent content 2.6 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.281 α = 90 b = 50.276 β = 90 c = 84.602 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 225 mm CCD 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 30 99.4 0.075 0.075 0.081 0.03 0.997 24.1 7 25567 -3 14.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 91.3 0.859 0.859 0.949 0.394 0.714 2.1 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 29.42 24144 1319 99.83 0.16548 0.16448 0.1656 0.18385 0.1854 RANDOM 16.069
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] 0.6 -1.11 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.022 r_long_range_B_refined 7.059 r_long_range_B_other 6.608 r_dihedral_angle_1_deg 5.99 r_scangle_other 3.297 r_scbond_it 2.128 r_scbond_other 2.095 r_dihedral_angle_2_deg 1.854 r_mcangle_it 1.771 r_mcangle_other 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.022 r_long_range_B_refined 7.059 r_long_range_B_other 6.608 r_dihedral_angle_1_deg 5.99 r_scangle_other 3.297 r_scbond_it 2.128 r_scbond_other 2.095 r_dihedral_angle_2_deg 1.854 r_mcangle_it 1.771 r_mcangle_other 1.77 r_angle_refined_deg 1.203 r_mcbond_it 1.05 r_mcbond_other 1.049 r_angle_other_deg 0.456 r_chiral_restr 0.073 r_gen_planes_refined 0.015 r_gen_planes_other 0.012 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 1082 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing