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Crystal structure of AMPylated GRP78 in apo form (Crystal form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 5% PEG1000, 0.1M Na2HPO4-Citrate, ph4.2, 0.2M LI2SO4
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.088 α = 90 b = 75.408 β = 90 c = 98.308 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2017-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
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 1.67 75.41 98.3 0.086 0.096 0.051 0.997 12 6.6 59490
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 1.67 1.7 100 0.794 0.861 0.464 0.888 2.1 6.7
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 5O4P 1.67 59.83 56476 3010 98.25 0.21305 0.21121 0.2233 0.24923 0.2559 RANDOM 23.139
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] -1.84 0.2 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.07 r_dihedral_angle_4_deg 15.255 r_dihedral_angle_3_deg 11.627 r_dihedral_angle_1_deg 5.241 r_long_range_B_refined 2.987 r_long_range_B_other 2.987 r_scangle_other 1.679 r_mcangle_it 1.532 r_mcangle_other 1.532 r_angle_refined_deg 1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.07 r_dihedral_angle_4_deg 15.255 r_dihedral_angle_3_deg 11.627 r_dihedral_angle_1_deg 5.241 r_long_range_B_refined 2.987 r_long_range_B_other 2.987 r_scangle_other 1.679 r_mcangle_it 1.532 r_mcangle_other 1.532 r_angle_refined_deg 1.184 r_scbond_it 1.003 r_scbond_other 1.002 r_mcbond_it 0.873 r_mcbond_other 0.872 r_angle_other_deg 0.867 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3967 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing