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Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 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: 22% 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 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.639 α = 90 b = 135.664 β = 97.37 c = 111.557 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 300 mm CCD BIOMORPH MIRRORS (KIRKPATRICK- BAEZ CONFIGURATION) 2011-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 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 1.81 50 98.3 0.093 16.7 6.5 164390 -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 1.81 1.84 80.9 0.41 2.3 2.9
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 (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 3L4M 1.81 35.01 159026 155734 8247 97.9 0.147 0.145 0.1624 0.187 0.2019 RANDOM 29.75
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] 0.03 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 15.649 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 6.667 r_scangle_it 4.565 r_scbond_it 3.044 r_angle_refined_deg 2.092 r_mcangle_it 1.854 r_mcbond_it 1.182 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 15.649 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 6.667 r_scangle_it 4.565 r_scbond_it 3.044 r_angle_refined_deg 2.092 r_mcangle_it 1.854 r_mcbond_it 1.182 r_chiral_restr 0.17 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 13241 Nucleic Acid Atoms Solvent Atoms 1824 Heterogen Atoms 198
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing