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Crystal Structure of the Quinone Form of Methylamine Dehydrogenase in Complex with the Diferric 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 VAPOR DIFFUSION, HANGING DROP 6.2 293 Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM WT-MauG and 50uM MADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 25% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.2., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.222 α = 64.77 b = 99.422 β = 74.77 c = 102.832 γ = 75.14
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) 2010-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
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 1.86 50 97.5 0.097 13.9 3.8 158031 154080 -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 1.86 1.89 95.8 0.472 3 3.7 7900
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 1.86 49.12 150636 146343 7734 97.15 0.13833 0.1362 0.1424 0.1782 0.1835 RANDOM 21.476
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.591 r_scangle_it 4.776 r_scbond_it 3.141 r_angle_refined_deg 2.142 r_mcangle_it 1.897 r_mcbond_it 1.207 r_chiral_restr 0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.591 r_scangle_it 4.776 r_scbond_it 3.141 r_angle_refined_deg 2.142 r_mcangle_it 1.897 r_mcbond_it 1.207 r_chiral_restr 0.177 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 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 13234 Nucleic Acid Atoms Solvent Atoms 2009 Heterogen Atoms 235
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing