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Crystal structure of M26V 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 9 298 100 mM Tris-HCl pH 9.0, 200 mM sodium acetate trihydrate, 25% PEG 4000 and 3 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.039 α = 90 b = 75.039 β = 90 c = 75.269 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic blue confocal optics 2014-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 1.45 65 99.7 0.062 56.6 20.4 43750 43750
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 1.45 1.5 97 0.523 5 18.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.45 64.99 43711 41569 2142 99.91 0.1114 0.11029 0.1093 0.13243 0.1319 RANDOM 20.241
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] 0.18 0.09 0.18 -0.58
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.022 r_dihedral_angle_2_deg 37.36 r_dihedral_angle_4_deg 18.149 r_sphericity_bonded 13.428 r_dihedral_angle_3_deg 11.882 r_dihedral_angle_1_deg 5.95 r_long_range_B_refined 5.783 r_scangle_other 4.626 r_long_range_B_other 4.537 r_scbond_it 3.953
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.022 r_dihedral_angle_2_deg 37.36 r_dihedral_angle_4_deg 18.149 r_sphericity_bonded 13.428 r_dihedral_angle_3_deg 11.882 r_dihedral_angle_1_deg 5.95 r_long_range_B_refined 5.783 r_scangle_other 4.626 r_long_range_B_other 4.537 r_scbond_it 3.953 r_scbond_other 3.921 r_rigid_bond_restr 3.14 r_mcangle_it 2.676 r_mcangle_other 2.602 r_mcbond_it 2.359 r_mcbond_other 2.136 r_angle_refined_deg 1.793 r_angle_other_deg 1.132 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 1391 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 20
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling