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Structure of the Mitomycin 7-O-methyltransferase MmcR with bound Mitomycin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWZ PDB entry 3GWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein Solution (10 mg/ml MmcR Protein,
0.05 M NaCl, 0.02 M Tris pH 8)
mixed in a 1:1 ratio with the Well Solution
(10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0)
Crystals were soaked with 5mM Mitomycin A for 8hrs
Cryoprotected with 25% ethylene glycol, 10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.841 α = 90 b = 98.844 β = 90 c = 171.045 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors and beryllium lenses 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.3 50 88.8 0.092 11.332 3.9 59548
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 2.3 2.38 70.7 0.315 3.861 3.3
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 3GWZ 2.3 43.92 59450 3003 88.8 0.205 0.202 0.2001 0.255 0.2525 36.51
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] 3.716 -1.072 -2.711
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.345 f_angle_d 1.102 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10296 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 206
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling