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Crystal Structure of the P107S-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 VAPOR DIFFUSION, HANGING DROP 6.4 293 Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM P107S-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 22% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.606 α = 67.05 b = 89.001 β = 79.51 c = 104.812 γ = 79.72
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) 2011-03-30 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 1.63 50 92.5 0.051 24.2 3.7 225455 208546 -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 1.63 1.66 58.6 0.292 2.9 2.6 11312
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 1.63 29.39 214346 198077 10468 92.41 0.14386 0.14197 0.1603 0.17952 0.1889 RANDOM 22.234
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] -0.11 0.08 -0.01 -0.02 0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 6.545 r_scangle_it 4.704 r_scbond_it 3.174 r_angle_refined_deg 2.354 r_mcangle_it 2.079 r_mcbond_it 1.363 r_chiral_restr 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 6.545 r_scangle_it 4.704 r_scbond_it 3.174 r_angle_refined_deg 2.354 r_mcangle_it 2.079 r_mcbond_it 1.363 r_chiral_restr 0.23 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 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 13106 Nucleic Acid Atoms Solvent Atoms 1966 Heterogen Atoms 223
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing