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Crystal structure of the binary complex of photosyntetic A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with cp12-2, both from Arabidopsis thaliana.
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, SITTING DROP 6.5 277 15% (w/v) PEG 4K, 0.6 M NaCl, 1 mM NAD and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.67 α = 90 b = 245.99 β = 90 c = 138.66 γ = 90
Symmetry Space Group C 2 2 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 2007-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 34.2 99.2 0.139 0.139 5.9 3.3 168053 163587 3 3 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.08 98.2 0.716 0.716 1.3 3.2 24070
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-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 3K2B 2 34.2 153928 153928 8137 99.04 0.22776 0.22776 0.22537 0.2327 0.27243 0.277 RANDOM 30.638
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] -2.31 -0.67 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.578 r_dihedral_angle_4_deg 19.599 r_dihedral_angle_3_deg 18.292 r_dihedral_angle_1_deg 7.094 r_mcangle_it 1.801 r_angle_refined_deg 1.737 r_scangle_it 1.595 r_mcbond_it 1.47 r_scbond_it 1.107 r_angle_other_deg 0.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.578 r_dihedral_angle_4_deg 19.599 r_dihedral_angle_3_deg 18.292 r_dihedral_angle_1_deg 7.094 r_mcangle_it 1.801 r_angle_refined_deg 1.737 r_scangle_it 1.595 r_mcbond_it 1.47 r_scbond_it 1.107 r_angle_other_deg 0.824 r_symmetry_vdw_other 0.297 r_symmetry_hbond_refined 0.284 r_mcbond_other 0.28 r_symmetry_vdw_refined 0.272 r_nbd_other 0.226 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.185 r_nbtor_other 0.097 r_chiral_restr 0.095 r_xyhbond_nbd_other 0.065 r_symmetry_hbond_other 0.064 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15827 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 299
Software Software Software Name Purpose DNA data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling