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Crystal structure of the essential protein PcsB from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 CRYSTALS GREW IN 2UL DROPLETS FORMED BY MIXING 1 UL OF PROTEIN SOLUTION AT 10 MG ML-1 (BUFFERED IN 20 MM TRIS-HCL PH 7.5) AND 1 UL L OF PRECIPITANT SOLUTION FORMED BY 12% (V/V) POLYETHYLENGLYCOL 4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE IN 1:1 VOLUME RATIO
Crystal Properties Matthews coefficient Solvent content 3.9 68.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.815 α = 90 b = 125.815 β = 90 c = 126.637 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.55 44.63 99.9 0.08 11.9 10.6 38172 2
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 2.55 2.66 99.8 0.64 2.9 11
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 THROUGHOUT NONE 2.55 44.63 36230 1907 99.85 0.23933 0.23761 0.2384 0.27173 0.2681 RANDOM 77.41
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] 36.7 36.7 -73.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.928 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_4_deg 13.793 r_dihedral_angle_1_deg 4.232 r_mcangle_it 2.642 r_angle_other_deg 1.709 r_mcbond_it 1.447 r_mcbond_other 1.447 r_scbond_it 1.124 r_angle_refined_deg 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.928 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_4_deg 13.793 r_dihedral_angle_1_deg 4.232 r_mcangle_it 2.642 r_angle_other_deg 1.709 r_mcbond_it 1.447 r_mcbond_other 1.447 r_scbond_it 1.124 r_angle_refined_deg 0.834 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5222 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SHELX phasing