☰ Navigation Tabs
1.65 Angstrom Crystal Structure of Serine-rich Repeat Adhesion Glycoprotein (Srr1) from Streptococcus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R17 PDB entry 1R17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl, pH 8.3. Screen: PACT (B11), 0.2M Calcium chloride, 0.1M Tris-HCl, pH 6.0, 20% (w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.356 α = 90 b = 83.235 β = 90 c = 57.056 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD Mirrors 2013-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97928 APS 21-ID-D
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 1.65 30 99.5 0.058 26.4 6 42747 42747 -3 20.1
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 1.65 1.68 100 0.5 3.8 6.1 2121
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 1R17 1.65 28.93 40447 40447 2141 99.52 0.15537 0.15375 0.1652 0.18721 0.2008 RANDOM 24.064
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] 0.04 -0.81 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.732 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 10.203 r_long_range_B_refined 6.788 r_long_range_B_other 6.605 r_dihedral_angle_1_deg 4.656 r_scangle_other 3.499 r_mcangle_it 2.407 r_mcangle_other 2.406 r_scbond_it 2.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.732 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 10.203 r_long_range_B_refined 6.788 r_long_range_B_other 6.605 r_dihedral_angle_1_deg 4.656 r_scangle_other 3.499 r_mcangle_it 2.407 r_mcangle_other 2.406 r_scbond_it 2.325 r_scbond_other 2.324 r_angle_refined_deg 1.554 r_mcbond_it 1.518 r_mcbond_other 1.515 r_angle_other_deg 0.696 r_chiral_restr 0.091 r_gen_planes_refined 0.017 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling