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Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG, C2 Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SXT PDB entry 3SXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein mixture: 100uM reduced WT-MauG and 50uM reduced MADH in 10mM potassium phosphate pH7.5 with 2mM sodium dithionite. Reservoir solution contained: 24% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4 and 2mM sodium dithionite. Crystallization was carried out in an anaerobic glove box at ambient temperature., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 346.356 α = 90 b = 55.558 β = 106.55 c = 112.548 γ = 90
Symmetry Space Group C 1 2 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 300 mm CCD BIOMORPH MIRRORS (KIRKPATRICK- BAEZ CONFIGURATION) 2010-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
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 50 99.8 0.104 13.55 4.8 132241 -3
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 2.03 99.5 0.551 2.65 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3SXT 2 43.06 132241 131712 6968 99.6 0.14602 0.14602 0.14369 0.1551 0.19013 0.1975 RANDOM 29.748
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] -0.1 0.1 -0.2 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.557 r_dihedral_angle_4_deg 17.723 r_dihedral_angle_3_deg 14.604 r_dihedral_angle_1_deg 6.711 r_angle_refined_deg 2.065 r_angle_other_deg 0.944 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.557 r_dihedral_angle_4_deg 17.723 r_dihedral_angle_3_deg 14.604 r_dihedral_angle_1_deg 6.711 r_angle_refined_deg 2.065 r_angle_other_deg 0.944 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13249 Nucleic Acid Atoms Solvent Atoms 1707 Heterogen Atoms 198
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling