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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 2.02 39.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.025 α = 90 b = 108.681 β = 105.81 c = 90.986 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 CCD ADSC QUANTUM 315r Mirrors 2015-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.10 SSRL BL12-2
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 2.85 87.55 99.7 0.057 9.6 3.7 29605 42.6
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 2.85 2.9 99.7 0.241 3.7
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 2.85 87.55 27610 1969 98.82 0.1767 0.17419 0.1772 0.21164 0.2129 RANDOM 43.017
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] -0.04 -0.02 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 5.987 r_long_range_B_refined 5.513 r_long_range_B_other 5.51 r_scangle_other 3.331 r_mcangle_it 3.05 r_mcangle_other 3.05 r_scbond_it 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 5.987 r_long_range_B_refined 5.513 r_long_range_B_other 5.51 r_scangle_other 3.331 r_mcangle_it 3.05 r_mcangle_other 3.05 r_scbond_it 1.98 r_scbond_other 1.98 r_mcbond_it 1.838 r_mcbond_other 1.838 r_angle_refined_deg 1.333 r_angle_other_deg 1.143 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 10069 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing