3MMH

X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2529323% MPD, 120 mM Mg(CH3COO)2, 100 mM cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.32α = 104.17
b = 39.48β = 105.16
c = 52.25γ = 100.5
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.886SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.22584.40.03919.918.5475066-318.941
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.2337.40.4183.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.25207091235451000.120.1180.157RANDOM19.68
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]
0.30.090.08-0.030.01-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg17.203
r_dihedral_angle_3_deg12.176
r_dihedral_angle_1_deg7.406
r_scangle_it6.8
r_scbond_it5.065
r_mcangle_it3.516
r_mcbond_it2.488
r_angle_refined_deg2.286
r_rigid_bond_restr2.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg17.203
r_dihedral_angle_3_deg12.176
r_dihedral_angle_1_deg7.406
r_scangle_it6.8
r_scbond_it5.065
r_mcangle_it3.516
r_mcbond_it2.488
r_angle_refined_deg2.286
r_rigid_bond_restr2.258
r_angle_other_deg1.24
r_mcbond_other0.865
r_chiral_restr0.285
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2564
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms69

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction