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perdeuterated human DJ-1, 100K
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 7.5 295 22-24% PEG 3000, 200 mM NaCl, and 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.02 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.836 α = 90 b = 74.836 β = 90 c = 75.347 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 2020-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.729 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.92 37.67 99.9 1 18.2 11 168364 9.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.92 0.94 0.332
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.92 37.42 1.34 167834 5069 99.6 0.1041 0.1039 0.105 0.1125 0.1138 16.16
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.5162 f_angle_d 1.0082 f_chiral_restr 0.0799 f_plane_restr 0.0096 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1391 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing