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Crystal Structure of C150A mutant of Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli at 1.98 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 6.3 293 100mM sodium Cacodylate pH 6.3, 18% (w/v)PEG 1000, 200mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.087 α = 90 b = 90.087 β = 90 c = 340.867 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 2016-09-19 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 1.98 50.01 90.9 0.17 10.9 8.7 89856
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 1.98 2.01 87.2 0.565 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C5F 1.98 50.01 85610 4399 90.87 0.15012 0.14766 0.19847 0.1951 RANDOM 20.507
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] 0.23 0.23 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.816 r_dihedral_angle_4_deg 20.825 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.107 r_long_range_B_refined 5.509 r_long_range_B_other 5.485 r_scangle_other 4.083 r_scbond_it 2.614 r_scbond_other 2.613 r_mcangle_other 2.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.816 r_dihedral_angle_4_deg 20.825 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.107 r_long_range_B_refined 5.509 r_long_range_B_other 5.485 r_scangle_other 4.083 r_scbond_it 2.614 r_scbond_other 2.613 r_mcangle_other 2.215 r_mcangle_it 2.214 r_angle_refined_deg 1.87 r_mcbond_it 1.524 r_mcbond_other 1.523 r_angle_other_deg 1.024 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 10093 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing