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Mth0212 in complex with a short ssDNA (CGTA)
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 7 293 reservoir: 25% MPD, 100mM KHEPES pH 7.0; complex solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.325 α = 90 b = 80.325 β = 90 c = 79.611 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 100 CCD MAR CCD 165 mm 2007-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81500 EMBL/DESY, HAMBURG X11
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 2.3 30 99.8 0.085 17.1 5.5 25521 44.8
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 2.3 2.38 99.3 0.347 4.1 4.5
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 2.3 28.27 25486 1295 99.7 0.207 0.204 0.2029 0.263 0.2616 RANDOM 38.834
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] -0.9 -0.45 -0.9 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.327 r_dihedral_angle_3_deg 19.038 r_dihedral_angle_4_deg 18.198 r_dihedral_angle_1_deg 7.606 r_scangle_it 2.698 r_scbond_it 1.69 r_angle_refined_deg 1.556 r_mcangle_it 1.414 r_mcbond_it 0.804 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.327 r_dihedral_angle_3_deg 19.038 r_dihedral_angle_4_deg 18.198 r_dihedral_angle_1_deg 7.606 r_scangle_it 2.698 r_scbond_it 1.69 r_angle_refined_deg 1.556 r_mcangle_it 1.414 r_mcbond_it 0.804 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.156 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4273 Nucleic Acid Atoms 83 Solvent Atoms 168 Heterogen Atoms 59
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling