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Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DRUVRD FORM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.1 M NA-FLUORIDE
Crystal Properties Matthews coefficient Solvent content 2.75 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.489 α = 90 b = 89.785 β = 89.97 c = 293.798 γ = 90
Symmetry Space Group P 1 21 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3 66.2 89 0.06 6.5 1.5 62649 72.3
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 3 3.16 86.5 0.32 1.9 1.4
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 DRUVRD FORM1 3 66.18 59507 3128 87.23 0.23114 0.2282 0.2305 0.28783 0.2876 RANDOM 104.631
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] 7.5 -0.01 -0.6 -6.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_1_deg 8.292 r_angle_refined_deg 1.544 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_1_deg 8.292 r_angle_refined_deg 1.544 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 20008 Nucleic Acid Atoms 1876 Solvent Atoms 97 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing