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The structure of the stress response protein DR1199 from Deinococcus radiodurans: a member of the DJ-1 superfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GSI PDB ENTRY 1GSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 0.2 M MAGNESIUM FORMATE PH 5.9, 20% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.838 α = 90 b = 88.562 β = 90 c = 64.088 γ = 90
Symmetry Space Group P 21 21 2
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 CCD TOROIDAL MIRROR 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.15 20 99.8 0.08 20.5 6.9 20998 4
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 2.15 2.27 99.9 0.52 3 6.8
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 PDB ENTRY 1GSI 2.15 19.94 19890 1077 100 0.203 0.2 0.1981 0.261 0.2544 RANDOM 22.31
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] 0.9 -0.72 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.33 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_1_deg 6.049 r_scangle_it 1.913 r_scbond_it 1.322 r_angle_refined_deg 1.313 r_mcangle_it 0.728 r_mcbond_it 0.435 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.33 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_1_deg 6.049 r_scangle_it 1.913 r_scbond_it 1.322 r_angle_refined_deg 1.313 r_mcangle_it 0.728 r_mcbond_it 0.435 r_nbtor_refined 0.297 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2778 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing