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Crystal structure of accessory secretory protein 1,2 and 3 in Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M Tris pH 8.0, 15% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.158 α = 90 b = 101.158 β = 90 c = 196.851 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 CCD ADSC QUANTUM 315r 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.9 50 99.85 0.991 12.25 4.7 26531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 0.833
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 MOLECULAR REPLACEMENT THROUGHOUT 5vae 2.9 42.94 25180 1310 99.85 0.1993 0.1971 0.1904 0.2416 0.2374 RANDOM 32.37
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] -0.22 -0.11 -0.22 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.204 r_dihedral_angle_4_deg 26.075 r_dihedral_angle_3_deg 17.997 r_dihedral_angle_1_deg 6.802 r_angle_other_deg 3.561 r_angle_refined_deg 1.298 r_chiral_restr 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.204 r_dihedral_angle_4_deg 26.075 r_dihedral_angle_3_deg 17.997 r_dihedral_angle_1_deg 6.802 r_angle_other_deg 3.561 r_angle_refined_deg 1.298 r_chiral_restr 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6407 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing