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The crystal structure of I-DmoI in complex with DNA and Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VS7 PDB ENTRY 2VS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6% PEG 4000, 0.07M SODIUM ACETATE, PH 4.6-5.5, 30% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 4.15 73.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.134 α = 90 b = 70.634 β = 119.85 c = 106.955 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.1 26.82 99.7 0.05 12.8 3 80887 2
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 2.1 2.21 99.5 0.45 2.3 2.8
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 2VS7 2.1 25.76 76811 4048 99.7 0.203 0.201 0.1907 0.248 0.2344 RANDOM 46.71
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] -0.08 -0.03 0.13 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_1_deg 17.584 r_dihedral_angle_4_deg 17.309 r_dihedral_angle_3_deg 15.492 r_scangle_it 4.037 r_scbond_it 2.89 r_mcangle_it 2.404 r_angle_refined_deg 1.698 r_mcbond_it 1.455 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_1_deg 17.584 r_dihedral_angle_4_deg 17.309 r_dihedral_angle_3_deg 15.492 r_scangle_it 4.037 r_scbond_it 2.89 r_mcangle_it 2.404 r_angle_refined_deg 1.698 r_mcbond_it 1.455 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.229 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.215 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_refined 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 4534 Nucleic Acid Atoms 3063 Solvent Atoms 392 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing