☰ Navigation Tabs
GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.885 α = 90 b = 124.455 β = 99.39 c = 141.986 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) 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 1.52 140.09 69.4 0.08 0.09 0.03 0.997 11.7 6.9 295271 23.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.71 12.2 1.071 1.161 0.444 0.608 1.7 6.8
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 1U8F 1.525 140.09 295271 14686 69.4 0.1829 0.182 0.1995 0.1998 RANDOM 27.48
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] -0.1084 -0.0028 0.1391 -0.0306
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.34 t_omega_torsion 3.79 t_angle_deg 1.02 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.34 t_omega_torsion 3.79 t_angle_deg 1.02 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20156 Nucleic Acid Atoms Solvent Atoms 1639 Heterogen Atoms 272
Software Software Software Name Purpose BUSTER refinement PROCOR data reduction Aimless data scaling MOLREP phasing