☰ Navigation Tabs
Joint Xray/Neutron structure of human DJ-1 at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
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 7.5 289 20% PEG3350, 100 mM HEPES pH=7.5 and 200 mM KCl
Crystal Properties Matthews coefficient Solvent content 2.92 57.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.41 α = 90 b = 67.41 β = 90 c = 179.791 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 IMAGE PLATE RIGAKU RAXIS IV++ 2019-10-15 M SINGLE WAVELENGTH 2 1 neutron 295 SCINTILLATION ORNL ANGER CAMERA 2019-09-11 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.542 2 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.00-4.16 ORNL Spallation Neutron Source MANDI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.63 48.96 99.8 0.991 21.4 6.7 31092 25.62 2 2.15 14.82 88.6 0.95 9.7 9.4 12347 25.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 0.833 2 2.15 2.23 0.49
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.63 33.13 1.35 31054 1580 99.61 0.1345 0.1334 0.1354 0.1548 0.1583 43.07 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.15 14.09 12346 88.03 0.2318 0.2813
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 20.647 f_dihedral_angle_d 20.647 f_angle_d 1.462 f_angle_d 1.462 f_chiral_restr 0.078 f_chiral_restr 0.078 f_bond_d 0.011 f_bond_d 0.011 f_plane_restr 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1420 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement