4M3P

Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LT8PDB ENTRY 1LT8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.527720.0% PEG5000 MME, 0.2 M sodium/potassium tartrate, 1.4% 1,2,3-heptanetriol, pH 7.5, EVAPORATION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3146.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.097α = 90
b = 102.617β = 101.76
c = 96.228γ = 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 focusing2006-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.89545.22298.20.0830.07213.74.112986212858234.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8952.01900.3740.36944.119787

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 1LT81.89545.222123327122106647699.010.182140.180210.21852RANDOM33.943
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]
-0.140.422.05-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.218
r_dihedral_angle_4_deg17.951
r_dihedral_angle_3_deg15.009
r_dihedral_angle_1_deg5.516
r_angle_refined_deg1.356
r_angle_other_deg0.806
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.218
r_dihedral_angle_4_deg17.951
r_dihedral_angle_3_deg15.009
r_dihedral_angle_1_deg5.516
r_angle_refined_deg1.356
r_angle_other_deg0.806
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11469
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms60

Software

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