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Crystal structure of human GRP78 in complex with 8-aminoadenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Triclinic crystals of apo GRP78 were observed in 0.1 M Tris-HCl, 25% PEG3350, 0.1 M sodium/potassium tartrate. Initial crystals were then microseeded in 25% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride. These new apo monoclinic crystals were soaked with 5 mM 8-aminoadenosine for one week.
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.662 α = 90 b = 74.775 β = 99.48 c = 89.485 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 173 PIXEL DECTRIS PILATUS 6M 2017-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03327 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.14 88.263 99.2 0.1 0.108 0.041 12.3 6.8 39667 37.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.26 95.4 0.639 0.639 0.694 0.268 1.2 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.14 31.17 39640 1922 98.9 0.189 0.187 0.1921 0.231 0.2324 RANDOM 40.5
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] -15.2358 4.9818 4.6603 10.5755
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.9 t_omega_torsion 2.92 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.9 t_omega_torsion 2.92 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 5930 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing BUSTER refinement PDB_EXTRACT data extraction