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X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 3.0-3.5 M ammonium sulphate, 0.1 M Na-Hepes.
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.849 α = 90 b = 76.849 β = 90 c = 406.626 γ = 120
Symmetry Space Group P 61 2 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 2011-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.18 101.66 99.7 0.129 0.129 8.4 8.1 38786 3 -3
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 2.18 2.3 98.4 0.454 2.2 6
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 3K2B 2.3 67.77 31304 1653 99.66 0.2508 0.2493 0.2777 0.2623 RANDOM 47.534
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] 3.46 1.73 3.46 -5.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_3_deg 22.591 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_1_deg 6.873 r_scangle_it 3.787 r_scbond_it 2.4 r_angle_refined_deg 1.94 r_mcangle_it 1.914 r_mcbond_it 1.088 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_3_deg 22.591 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_1_deg 6.873 r_scangle_it 3.787 r_scbond_it 2.4 r_angle_refined_deg 1.94 r_mcangle_it 1.914 r_mcbond_it 1.088 r_chiral_restr 0.118 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5127 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 123
Software Software Software Name Purpose iMOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction