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Crystal structure of the binary complex of RecD2 with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E1S PDB entry 3E1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 15% PEG 8000, 2-6% Ethylene glycol, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.14 α = 90 b = 90.32 β = 90 c = 142.18 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 50 98.8 0.032 0.032 33.7 4.9 24877 24589 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 91.8 0.175 0.175 8 4.3 2492
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 (All) 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 3E1S 2.5 45.18 23332 23332 1256 98.99 0.23023 0.23023 0.22815 0.2298 0.26827 0.2676 RANDOM 37.8
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.779 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 17.75 r_dihedral_angle_1_deg 5.212 r_angle_refined_deg 1.146 r_angle_other_deg 0.885 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.208 r_nbd_other 0.196 r_symmetry_vdw_other 0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.779 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 17.75 r_dihedral_angle_1_deg 5.212 r_angle_refined_deg 1.146 r_angle_other_deg 0.885 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.208 r_nbd_other 0.196 r_symmetry_vdw_other 0.195 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.086 r_symmetry_vdw_refined 0.045 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_chiral_restr r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 4088 Nucleic Acid Atoms 157 Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling