3SXT | pdb_00003sxt

Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L4M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.4293Drops 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 coefficientSolvent content
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.639α = 90
b = 135.664β = 97.37
c = 111.557γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBIOMORPH MIRRORS (KIRKPATRICK- BAEZ CONFIGURATION)2011-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.815098.30.09316.76.5164390-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8480.90.412.32.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3L4M1.8135.01159026155734824797.90.1470.1450.160.1870.2RANDOM29.75
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.389
r_dihedral_angle_4_deg15.649
r_dihedral_angle_3_deg13.751
r_dihedral_angle_1_deg6.667
r_scangle_it4.565
r_scbond_it3.044
r_angle_refined_deg2.092
r_mcangle_it1.854
r_mcbond_it1.182
r_chiral_restr0.17
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13241
Nucleic Acid Atoms
Solvent Atoms1824
Heterogen Atoms198

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing