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Crystal Structure of the Y294H-MauG/pre-Methylamine Dehydrogenase Complex
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 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG 8000, 0.1 M sodium acetate, 0.1 M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.527 α = 109.94 b = 83.524 β = 91.54 c = 107.782 γ = 105.78
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) 2009-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 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 1.91 50 95.6 0.08 13.6 3.7 132062 126251 -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 1.91 1.95 70.6 0.425 2 2.2 6557
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 1.91 44.49 127728 119911 6318 93.9 0.141 0.139 0.157 0.187 0.2016 RANDOM BASED ON R-FREE FOR 3L4M 28.71
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 0.04 -0.01 0.06 0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 18.696 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 6.427 r_scangle_it 5.023 r_scbond_it 3.311 r_angle_refined_deg 2.078 r_mcangle_it 1.978 r_mcbond_it 1.187 r_chiral_restr 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 18.696 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 6.427 r_scangle_it 5.023 r_scbond_it 3.311 r_angle_refined_deg 2.078 r_mcangle_it 1.978 r_mcbond_it 1.187 r_chiral_restr 0.192 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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 13215 Nucleic Acid Atoms Solvent Atoms 1301 Heterogen Atoms 262
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing