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Direct visualisation of strain-induced protein post-translational modification
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZD PDB ENTRY 4AZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.27 α = 90 b = 86.27 β = 90 c = 80.81 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU R-AXIS IV VARIMAX OPTICS 2013-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 33.7 99.5 0.18 5.7 3.2 17250 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.8 0.62 1.8 3.1
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 PDB ENTRY 4AZD 2.1 33.69 16351 871 99.25 0.17523 0.17209 0.1495 0.23688 0.1898 RANDOM 26.268
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] -4.5 -4.5 8.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.769 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 15.287 r_dihedral_angle_1_deg 8.399 r_mcangle_it 4.023 r_scbond_it 3.336 r_mcbond_it 2.616 r_mcbond_other 2.593 r_angle_refined_deg 2.094 r_angle_other_deg 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.769 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 15.287 r_dihedral_angle_1_deg 8.399 r_mcangle_it 4.023 r_scbond_it 3.336 r_mcbond_it 2.616 r_mcbond_other 2.593 r_angle_refined_deg 2.094 r_angle_other_deg 0.91 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing