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Structures of Streptococcus agalactiae GBS GAPDH in different enzymatic states
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QX6 4QX6_A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 20-28% PEG4000, 0.1M Mes
Crystal Properties Matthews coefficient Solvent content 2.06 40.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.578 α = 90 b = 107.465 β = 104.07 c = 89.273 γ = 90
Symmetry Space Group P 1 21 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 Mirrors 2014-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 86.6 99.3 0.084 0.987 11.3 2.5 82890 24.5
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 2.11 99.1 0.467 1.9 2.5
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 4QX6_A 2 86.6 78706 4145 99.23 0.19597 0.19488 0.2011 0.21625 0.2208 RANDOM 29.477
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 20.341 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.133 r_long_range_B_refined 4.402 r_long_range_B_other 4.326 r_scangle_other 2.836 r_mcangle_it 2.195 r_mcangle_other 2.195 r_scbond_it 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 20.341 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.133 r_long_range_B_refined 4.402 r_long_range_B_other 4.326 r_scangle_other 2.836 r_mcangle_it 2.195 r_mcangle_other 2.195 r_scbond_it 1.751 r_scbond_other 1.751 r_mcbond_it 1.363 r_mcbond_other 1.362 r_angle_refined_deg 1.36 r_angle_other_deg 1.064 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10020 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing