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Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.35 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 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.339 α = 90 b = 90.339 β = 90 c = 341.547 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 2.35 50.01 100 0.19 14 11.3 60156
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 2.35 2.39 100 0.624 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 7C5F 2.35 50 56884 3003 99.46 0.15778 0.15497 0.1645 0.20975 0.2129 RANDOM 32.346
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] 1.08 1.08 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 7.227 r_long_range_B_refined 6.034 r_long_range_B_other 6.033 r_scangle_other 4.474 r_mcangle_other 3.343 r_mcangle_it 3.341 r_scbond_it 3.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 7.227 r_long_range_B_refined 6.034 r_long_range_B_other 6.033 r_scangle_other 4.474 r_mcangle_other 3.343 r_mcangle_it 3.341 r_scbond_it 3.046 r_scbond_other 3.041 r_mcbond_it 2.245 r_mcbond_other 2.238 r_angle_refined_deg 1.793 r_angle_other_deg 1.012 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 10083 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing