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3.65 Angstrom Crystal Structure of Serine-rich Repeat Protein (Srr2) from Streptococcus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MBO PDB entry 4MBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.5mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl, pH 8.3. Screen: Trap96 (A11), 5M Sodium cloride. Cryo: 4M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 5.36 77.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.598 α = 90 b = 97.598 β = 90 c = 173.269 γ = 90
Symmetry Space Group P 41 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 Beryllium lenses 2012-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 3.65 30 99.9 0.05 41 9.4 9911 9911 -3 36.8
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 3.65 3.71 100 0.69 3.3 9.9 480
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 4MBO 3.65 29.62 9353 9353 471 99.63 0.21465 0.21336 0.2102 0.24073 0.2394 RANDOM 195.612
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] -1.67 -1.67 3.35
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 18.125 r_long_range_B_refined 18.122 r_scangle_other 14.207 r_dihedral_angle_2_deg 12.122 r_mcangle_it 11.957 r_mcangle_other 11.957 r_scbond_it 9.373 r_scbond_other 9.369 r_mcbond_it 7.845 r_mcbond_other 7.836
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 18.125 r_long_range_B_refined 18.122 r_scangle_other 14.207 r_dihedral_angle_2_deg 12.122 r_mcangle_it 11.957 r_mcangle_other 11.957 r_scbond_it 9.373 r_scbond_other 9.369 r_mcbond_it 7.845 r_mcbond_other 7.836 r_dihedral_angle_3_deg 6.43 r_dihedral_angle_4_deg 5.406 r_angle_refined_deg 1.724 r_dihedral_angle_1_deg 1.198 r_angle_other_deg 0.855 r_chiral_restr 0.101 r_gen_planes_refined 0.019 r_gen_planes_other 0.017 r_bond_refined_d 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling