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Atomic resolution structure of D24N 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 23-27% polyethylene glycol (PEG) 4000, 0.2 M Sodium Citrate, and 0.1 M Tris HCl
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.969 α = 90 b = 74.969 β = 90 c = 75.336 γ = 120
Symmetry Space Group P 31 2 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 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 38 99.8 0.042 1 20.4 5.5 98874
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 97.1 0.919 0.738 1.8 5.4
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 38 93885 4940 99.73 0.11387 0.11317 0.1129 0.12765 0.1273 RANDOM 16.762
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] 0.13 0.07 0.13 -0.43
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.178 r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 19.112 r_sphericity_bonded 12.384 r_dihedral_angle_3_deg 11.372 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 4.344 r_rigid_bond_restr 3.942 r_long_range_B_other 3.565 r_scangle_other 3.127
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.178 r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 19.112 r_sphericity_bonded 12.384 r_dihedral_angle_3_deg 11.372 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 4.344 r_rigid_bond_restr 3.942 r_long_range_B_other 3.565 r_scangle_other 3.127 r_scbond_it 2.584 r_scbond_other 2.576 r_mcangle_other 2.083 r_mcangle_it 2.075 r_mcbond_it 1.725 r_angle_refined_deg 1.699 r_mcbond_other 1.68 r_angle_other_deg 1.029 r_chiral_restr 0.138 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 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 1372 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing