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Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang
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 5.8 293 reservoir: 5% (w/v) PEG 4000, 50mM KCl, 50mM MES pH 5.8, 10mM MgCl2 ; complex solution: 240mM NaCl, 8mM HEPES-KOH pH 7.6, 4mM DTT, 2mM MgCl2, 1mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.603 α = 90 b = 81.301 β = 90 c = 97.091 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 MAR CCD 165 mm 2007-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81500 EMBL/DESY, HAMBURG X13
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 50 93.8 0.055 18 2.9 29120
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 76.3 0.191 4.2 2.6
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 48.55 27632 1470 93.55 0.21747 0.21421 0.2101 0.27938 0.2748 RANDOM 28.354
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] -1.79 0.12 -2.51 4.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.348 r_dihedral_angle_3_deg 16.774 r_dihedral_angle_4_deg 16.429 r_dihedral_angle_1_deg 6.509 r_scangle_it 2.291 r_scbond_it 1.45 r_angle_refined_deg 1.418 r_mcangle_it 1.062 r_mcbond_it 0.565 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.348 r_dihedral_angle_3_deg 16.774 r_dihedral_angle_4_deg 16.429 r_dihedral_angle_1_deg 6.509 r_scangle_it 2.291 r_scbond_it 1.45 r_angle_refined_deg 1.418 r_mcangle_it 1.062 r_mcbond_it 0.565 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4262 Nucleic Acid Atoms 501 Solvent Atoms 313 Heterogen Atoms 109
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