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Direct visualisation of strain-induced protein prost-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 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.28 α = 90 b = 86.28 β = 90 c = 80.88 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 1.7 33.7 99.7 0.04 13.3 2.4 32244 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 1.7 1.74 99.7 0.4 2.2 2.3
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 1.7 29.52 30609 1633 99.59 0.14611 0.14458 0.1573 0.17519 0.1891 RANDOM 23.383
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] -0.32 -0.32 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_4_deg 18.308 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 6.591 r_scbond_it 4.172 r_mcangle_it 3.931 r_mcbond_it 2.655 r_mcbond_other 2.652 r_angle_refined_deg 2.333 r_angle_other_deg 0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_4_deg 18.308 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 6.591 r_scbond_it 4.172 r_mcangle_it 3.931 r_mcbond_it 2.655 r_mcbond_other 2.652 r_angle_refined_deg 2.333 r_angle_other_deg 0.977 r_chiral_restr 0.144 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 2002 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing