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Crystal structure of an XPD DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSF PDB ENTRY 2VSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 50 MM MES (PH 6.5), 10 MM MGSO4, 5-30% 2-METHYL-2 4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.2 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.06 α = 90 b = 79.06 β = 90 c = 175.69 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 92 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.2 52 100 0.08 9.4 3.8 30961 -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 2.2 2.32 100 0.58 2.1 3.8
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 2VSF 2.2 39.53 29635 1545 99.02 0.19524 0.1923 0.195 0.25049 0.2531 RANDOM 40.218
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] 0.63 0.32 0.63 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 18.771 r_dihedral_angle_1_deg 6.629 r_angle_refined_deg 1.736 r_angle_other_deg 1.346 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 18.771 r_dihedral_angle_1_deg 6.629 r_angle_refined_deg 1.736 r_angle_other_deg 1.346 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4822 Nucleic Acid Atoms 83 Solvent Atoms 134 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing