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Crystal structure of lid-truncated ADP-bound BiP in an oligomeric state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.2 M potassium citrate tribasic monohydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.619433 53.07245
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.179 α = 90 b = 51.249 β = 99.77 c = 118.801 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 PILATUS3 6M 2020-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9762 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.94 29.27 99.1 0.999 13.7 3.3 43705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 94.5 0.717 2
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 6HAB 1.94 29.27 41507 2186 99.05 0.186 0.1839 0.1911 0.2264 0.2317 RANDOM 34.398
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] 1.58 -0.44 -1.35 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_1_deg 6.5 r_angle_refined_deg 1.333 r_angle_other_deg 1.233 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_1_deg 6.5 r_angle_refined_deg 1.333 r_angle_other_deg 1.233 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3937 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing