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Atomic resolution structure of E15Q mutant human DJ-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 25-28% PEG 4000, 0.1 M Tris HCl, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.276 α = 90 b = 121.963 β = 90 c = 43.512 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M Rh coated collimating mirror, K-B focusing mirrors 2016-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.88 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.1 37 98.1 0.07 0.999 14.9 5.1 91327
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 85.4 1.066 0.569 1.4 3.8
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 1p5f 1.1 37 88556 2751 97.91 0.11837 0.11777 0.1303 0.13735 0.15 RANDOM 13.225
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] 0.35 -0.44 0.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.608 r_dihedral_angle_2_deg 42.483 r_dihedral_angle_4_deg 17.445 r_sphericity_bonded 13.182 r_dihedral_angle_3_deg 11.549 r_long_range_B_refined 8.63 r_dihedral_angle_1_deg 6.327 r_long_range_B_other 5.384 r_rigid_bond_restr 2.126 r_angle_refined_deg 1.821
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.608 r_dihedral_angle_2_deg 42.483 r_dihedral_angle_4_deg 17.445 r_sphericity_bonded 13.182 r_dihedral_angle_3_deg 11.549 r_long_range_B_refined 8.63 r_dihedral_angle_1_deg 6.327 r_long_range_B_other 5.384 r_rigid_bond_restr 2.126 r_angle_refined_deg 1.821 r_scangle_other 1.572 r_scbond_other 1.393 r_scbond_it 1.392 r_mcangle_other 1.229 r_mcangle_it 1.214 r_angle_other_deg 1.046 r_mcbond_it 0.852 r_mcbond_other 0.809 r_chiral_restr 0.117 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1385 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing