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Complex of Mth0212 and an 8bp dsDNA with distorted ends
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FZI PDB ENTRY 3FZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 reservoir: 189mM KCl, 9.5mM MgCl2, 4.7% (w/v) PEG 8000, 47mM MES/NaOH pH 5.6, 2.1% 1,4-butanediol, 2mM DTT; protein solution: 234mM NaCl, 7mM KHEPES pH 7.6, 1.83mM MgCl2, 2.7mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.751 α = 90 b = 80.76 β = 94.03 c = 105.211 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 MARMOSAIC 225 mm CCD 2007-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97623 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 92.8 0.061 22.7 4.7 27308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 72.3 0.191 5.2 3.2
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 3FZI 2.4 44.64 27293 1391 92.72 0.1811 0.17782 0.1757 0.24286 0.2384 RANDOM 27.829
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] -0.7 1.12 -0.83 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 18.102 r_dihedral_angle_1_deg 7.201 r_scangle_it 2.84 r_scbond_it 1.788 r_angle_refined_deg 1.586 r_mcangle_it 1.328 r_mcbond_it 0.698 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 18.102 r_dihedral_angle_1_deg 7.201 r_scangle_it 2.84 r_scbond_it 1.788 r_angle_refined_deg 1.586 r_mcangle_it 1.328 r_mcbond_it 0.698 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4252 Nucleic Acid Atoms 423 Solvent Atoms 305 Heterogen Atoms 113
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling