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High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 23% PEG 300, 0.1 M Hepes, 15% isopropanol, and 5% glycerol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.549 α = 90 b = 147.403 β = 90 c = 147.669 γ = 90
Symmetry Space Group P 21 21 21
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 4 1999-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.97900 NSLS X8C
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 1.65 99 98 0.098 18.3 7 390958 2
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 1.65 1.69 85 0.397
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1CER 1.65 65.94 345630 364002 18372 100 0.159 0.158 0.1642 0.172 0.176 RANDOM 11.833
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] 0.97 -0.09 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.487 r_scangle_it 2.291 r_scbond_it 1.366 r_angle_refined_deg 1.236 r_angle_other_deg 0.802 r_mcangle_it 0.742 r_mcbond_it 0.398 r_symmetry_vdw_other 0.261 r_nbd_other 0.248 r_nbd_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.487 r_scangle_it 2.291 r_scbond_it 1.366 r_angle_refined_deg 1.236 r_angle_other_deg 0.802 r_mcangle_it 0.742 r_mcbond_it 0.398 r_symmetry_vdw_other 0.261 r_nbd_other 0.248 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.116 r_metal_ion_refined 0.116 r_symmetry_vdw_refined 0.114 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19752 Nucleic Acid Atoms Solvent Atoms 1586 Heterogen Atoms 389
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling CNS phasing