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Crystal Structure of C150S mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.69 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 100mM sodium PBS pH 6.1, 16%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.45 49.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.378 α = 90 b = 90.378 β = 90 c = 342.107 γ = 90
Symmetry Space Group P 41 21 2
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 2016-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97776 SSRF BL18U1
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 2.68 50 100 0.135 15.17 12.8 41105
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 2.68 2.73 100 0.487 3.6 11.8
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 7C5F 2.68 48.223 38893 2070 99.82 0.16171 0.15776 0.1636 0.23677 0.2411 RANDOM 36.518
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] 1.35 1.35 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.705 r_dihedral_angle_4_deg 19.486 r_dihedral_angle_3_deg 14.076 r_dihedral_angle_1_deg 7.136 r_long_range_B_refined 6.022 r_long_range_B_other 6.006 r_scangle_other 3.905 r_mcangle_other 3.248 r_mcangle_it 3.247 r_scbond_it 2.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.705 r_dihedral_angle_4_deg 19.486 r_dihedral_angle_3_deg 14.076 r_dihedral_angle_1_deg 7.136 r_long_range_B_refined 6.022 r_long_range_B_other 6.006 r_scangle_other 3.905 r_mcangle_other 3.248 r_mcangle_it 3.247 r_scbond_it 2.415 r_scbond_other 2.41 r_mcbond_it 2.03 r_mcbond_other 2.023 r_angle_refined_deg 1.604 r_angle_other_deg 0.964 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10079 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 243
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing