☰ Navigation Tabs
GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 MORPHEUS condition F9: 0.12M MORPHEUS monosaccharides solution , 0.1M MORPHEUS Buffer System 3, 30% v/v MORPHEUS Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.787 α = 90 b = 124.652 β = 117.04 c = 79.74 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2019-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 72.85 67.6 0.226 0.245 0.991 6.5 7 81465
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 2.05 12.8 1.488 1.618 0.456 1.5 6.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YND 1.853 72.85 81457 4059 67.6 0.1911 0.1903 0.1978 0.2066 0.216 RANDOM 30.35
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] 1.1261 0.5176 0.4886 -1.6147
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.61 t_omega_torsion 3.71 t_angle_deg 1.05 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10108 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 173
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling MOLREP phasing