3BQ5

Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T7LPDB ENTRY 1T7L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR BATCH, UNDER OIL8.529519.5% PEG 3350, 0.2M magnesium acetate, 2.5% ethylene glycol, 0.1M Tris-HCl, pH 8.5, VAPOR BATCH, UNDER OIL, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2344.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.229α = 90
b = 107.164β = 108.96
c = 107.667γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2006-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.9793APS23-ID-D

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
1247.499.80.06315.64.810460610439834.7
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)
22.121000.3984.44.815374

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1T7L247.4104606104398261099.80.2180.2170.2403RANDOM38.99
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]
1.9035.615-4.6322.729
RMS Deviations
KeyRefinement Restraint Deviation
fIHEDRAL16.341
fNGLE0.851
fHIRALITY0.061
fOND0.005
fLANARITY0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11230
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms26

Software

Software
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
EPMRphasing