3RPD

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82890.1M Imidazole:HCl pH 8.0, 1.0M Sodium Citrate Tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1943.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.099α = 90
b = 89.371β = 92.45
c = 86.526γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97942APS19-ID

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
11.55099.20.0888.14.4111443111443-3
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)
1.51.5398.80.4254.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.536.5110936105371556599.140.16490.163620.189RANDOM12.229
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]
-0.330.54-0.170.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.69
r_dihedral_angle_4_deg15.315
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg5.326
r_scangle_it3.757
r_scbond_it2.347
r_angle_refined_deg1.425
r_mcangle_it1.361
r_angle_other_deg0.905
r_mcbond_it0.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.69
r_dihedral_angle_4_deg15.315
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg5.326
r_scangle_it3.757
r_scbond_it2.347
r_angle_refined_deg1.425
r_mcangle_it1.361
r_angle_other_deg0.905
r_mcbond_it0.762
r_mcbond_other0.229
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5438
Nucleic Acid Atoms
Solvent Atoms944
Heterogen Atoms38

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building