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Crystal Structure of C150A mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with PO4 at 2.49 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, 20%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.679 α = 90 b = 89.679 β = 90 c = 341.261 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 2.48 50 100 0.196 12 19.2 50448
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 2.49 2.53 100 0.776 4
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 2.48 48.031 47513 2516 99.27 0.15821 0.15469 0.163 0.22337 0.2213 RANDOM 33.431
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] 0.91 0.91 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.386 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_3_deg 14.008 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.022 r_long_range_B_other 6.019 r_scangle_other 4.041 r_mcangle_it 3.297 r_mcangle_other 3.297 r_scbond_it 2.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.386 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_3_deg 14.008 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.022 r_long_range_B_other 6.019 r_scangle_other 4.041 r_mcangle_it 3.297 r_mcangle_other 3.297 r_scbond_it 2.545 r_scbond_other 2.545 r_mcbond_it 2.103 r_mcbond_other 2.101 r_angle_refined_deg 1.675 r_angle_other_deg 0.981 r_chiral_restr 0.087 r_bond_refined_d 0.013 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 10062 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing