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Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9Z PDB ENTRY 1G9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 4 MG/ML PROTEIN, 35% METHANOL, 0.1M NACACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.54 61.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.612 α = 90 b = 69.209 β = 95.46 c = 88.671 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.8 32.92 95.5 0.05 3.6 45123 2
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 1G9Z 1.8 32.92 45123 2399 95.5 0.149 0.147 0.1505 0.197 0.1967 RANDOM 37.39
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] 0.49 -0.02 0.21 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 23.052 r_dihedral_angle_3_deg 16.945 r_scangle_it 7.687 r_dihedral_angle_1_deg 7.56 r_scbond_it 6.204 r_mcangle_it 4.487 r_mcbond_it 3.387 r_angle_refined_deg 1.975 r_symmetry_hbond_refined 0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 23.052 r_dihedral_angle_3_deg 16.945 r_scangle_it 7.687 r_dihedral_angle_1_deg 7.56 r_scbond_it 6.204 r_mcangle_it 4.487 r_mcbond_it 3.387 r_angle_refined_deg 1.975 r_symmetry_hbond_refined 0.434 r_xyhbond_nbd_refined 0.336 r_nbtor_refined 0.319 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.246 r_chiral_restr 0.156 r_metal_ion_refined 0.065 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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_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 2448 Nucleic Acid Atoms 980 Solvent Atoms 394 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing