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Human DJ-1 complexed with Na-K-tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 295 1.5 M sodium potassium tartrate, 3.5 M ammonium sulfate, 0.1 M Na-Cacodylate
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.802 α = 90 b = 74.802 β = 90 c = 75.819 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 ADSC QUANTUM 270 2012-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.127 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.66 30 99.8 54.3 2.1 29365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.72 100 1.6
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 3BWE 1.66 20 27853 1485 99.71 0.14305 0.14199 0.1537 0.16391 0.1707 RANDOM 13.826
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.93 r_dihedral_angle_4_deg 18.336 r_dihedral_angle_3_deg 13.497 r_long_range_B_refined 6.712 r_long_range_B_other 6.516 r_dihedral_angle_1_deg 6.287 r_scangle_other 5.634 r_scbond_other 3.782 r_scbond_it 3.776 r_angle_refined_deg 2.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.93 r_dihedral_angle_4_deg 18.336 r_dihedral_angle_3_deg 13.497 r_long_range_B_refined 6.712 r_long_range_B_other 6.516 r_dihedral_angle_1_deg 6.287 r_scangle_other 5.634 r_scbond_other 3.782 r_scbond_it 3.776 r_angle_refined_deg 2.509 r_mcangle_it 2.131 r_mcangle_other 2.13 r_mcbond_it 1.455 r_mcbond_other 1.422 r_angle_other_deg 1.252 r_chiral_restr 0.446 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1362 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing