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Crystal structure of BiP V461F (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LDN 3LDN, 5E85 experimental model PDB 5E85 3LDN, 5E85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 8% PEG1000, 0.1M Tris-HCl pH8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.61 α = 90 b = 52.5 β = 97.34 c = 91.73 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 PILATUS 6M-F 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 2.08 50.2 99.2 0.029 0.039 1 16.5 3.4 28693
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 2.08 2.13 99.5 0.775 1.063 0.602 1.4 3.2
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 3LDN, 5E85 2.08 50.2 27313 1367 99.06 0.23833 0.23676 0.2422 0.27102 0.2763 RANDOM 52.145
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] -1.91 -1.88 1.13 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.832 r_dihedral_angle_3_deg 14.249 r_dihedral_angle_4_deg 12.831 r_dihedral_angle_1_deg 5.879 r_long_range_B_other 4.515 r_long_range_B_refined 4.514 r_mcangle_it 2.835 r_mcangle_other 2.835 r_scangle_other 2.707 r_mcbond_it 1.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.832 r_dihedral_angle_3_deg 14.249 r_dihedral_angle_4_deg 12.831 r_dihedral_angle_1_deg 5.879 r_long_range_B_other 4.515 r_long_range_B_refined 4.514 r_mcangle_it 2.835 r_mcangle_other 2.835 r_scangle_other 2.707 r_mcbond_it 1.653 r_mcbond_other 1.653 r_scbond_it 1.579 r_scbond_other 1.579 r_angle_refined_deg 1.208 r_angle_other_deg 1.072 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 3714 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing