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Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD1 Dimer of PDB ENTRY 1GD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG 3350, HEPES, K3-citrate, microseeding, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.7 α = 90 b = 98.5 β = 90 c = 183.1 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 IMAGE PLATE MARRESEARCH Mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.8 ESRF BM1A
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 2.4 17.93 96.6 0.034 58424 56521 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 86.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Dimer of PDB ENTRY 1GD1 2.4 17.93 58424 56188 2853 96.2 0.203 0.2029 0.239 0.2381 RANDOM 31.1
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] -9.17 0.15 9.02
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.44 c_bond_d 0.01 c_dihedral_angle_d c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10044 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 88
Software Software Software Name Purpose MAR345 data collection DENZO data reduction SCALEPACK data scaling TRUNCATE data reduction AMoRE phasing CNS refinement CCP4 data scaling