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cyanobacterial GAPDH with NADP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 100 mM Hepes pH7.0
16% PEG3350
4% Tacsimate
5 mM DL-Glyceraldehyde-3-phosphate
5 mM NADP+,
5 mM NADPH
5 mM 3-phosphoglycerate
1 unit phosphoglycerate kinase
Crystal Properties Matthews coefficient Solvent content 2.5 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.469 α = 90 b = 141.469 β = 90 c = 74.425 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS3 6M 2017-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.54 44.74 99.98 0.09574 0.09982 0.02803 0.999 13.92 12.6 111368 19.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.595 99.95 0.8891 0.2636 0.567 1.94 12.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3zdf 1.54 44.737 1.4 111368 5517 99.96 0.1649 0.1639 0.1651 0.1833 0.1846 random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.802 f_angle_d 0.89 f_chiral_restr 0.057 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5246 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing