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The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.1 M DL-Malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.74 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.57 α = 90 b = 74.57 β = 90 c = 74.956 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 CCD RIGAKU SATURN 944+ 2020-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.027 50 99.8 0.109 19.1 8 16019
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 2.03 2.07 0.506
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1pdv 2.027 26.446 16005 847 99.732 0.153 0.152 0.1614 0.1736 0.1775 27.223
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] 0.486 0.243 0.486 -1.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.381 r_dihedral_angle_4_deg 19.732 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.613 r_lrange_it 4.185 r_lrange_other 4.003 r_scangle_it 2.354 r_scangle_other 2.353 r_mcangle_it 1.561 r_mcangle_other 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.381 r_dihedral_angle_4_deg 19.732 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.613 r_lrange_it 4.185 r_lrange_other 4.003 r_scangle_it 2.354 r_scangle_other 2.353 r_mcangle_it 1.561 r_mcangle_other 1.56 r_scbond_it 1.432 r_scbond_other 1.431 r_angle_refined_deg 1.236 r_angle_other_deg 1.195 r_mcbond_it 0.949 r_mcbond_other 0.94 r_nbd_other 0.198 r_symmetry_nbd_refined 0.195 r_nbd_refined 0.185 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.135 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing