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Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, Form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PJR PDB ENTRY 3PJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.0, 0.2 M NA-NITRATE
Crystal Properties Matthews coefficient Solvent content 2.67 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.572 α = 90 b = 67.448 β = 90 c = 386.04 γ = 90
Symmetry Space Group P 21 21 21
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 4 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 2.55 47.4 100 0.07 20.4 7.3 56088
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 2.55 2.69 100 0.59 3.6 6.5
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 3PJR 2.55 47.74 56088 2971 99.87 0.2141 0.21143 0.2106 0.26651 0.2633 RANDOM 71.45
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] 0.07 -0.2 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.859 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 17.796 r_dihedral_angle_1_deg 9.154 r_angle_refined_deg 1.744 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.859 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 17.796 r_dihedral_angle_1_deg 9.154 r_angle_refined_deg 1.744 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 10328 Nucleic Acid Atoms 956 Solvent Atoms 186 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MrBUMP phasing