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Crystal structure of SP1746 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287.15 25% PEG4000, 0.15 M (NH4)2SO4, 0.1 M MES, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.051 α = 90 b = 69.051 β = 90 c = 88.266 γ = 120
Symmetry Space Group P 32 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 200K 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97915 SSRF BL19U1
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 1.7 59.8 92.9 1 41.2 18.4 25426
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 1.7 1.73 0.961
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 1.7 59.8 24269 1124 92.92 0.19094 0.18973 0.1895 0.21608 0.2165 RANDOM 28.762
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] 0.54 0.27 0.54 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.654 r_dihedral_angle_4_deg 22.103 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 4.914 r_long_range_B_refined 4.291 r_scbond_it 1.802 r_mcangle_it 1.547 r_angle_refined_deg 1.242 r_mcbond_it 0.982 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.654 r_dihedral_angle_4_deg 22.103 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 4.914 r_long_range_B_refined 4.291 r_scbond_it 1.802 r_mcangle_it 1.547 r_angle_refined_deg 1.242 r_mcbond_it 0.982 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 1563 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing