2JCK

Crystal structure of alpha-1,3 Galactosyltransferase (R365K) in complex with UDP and 2 manganese ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K4VPDB ENTRY 1K4V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1M TRIS-HCL, PH 8.0, 10% PEG 6000, AND 5% MPD
Crystal Properties
Matthews coefficientSolvent content
2.7655

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.824α = 90
b = 68.251β = 90.19
c = 44.732γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
11.85091.70.194.53445713.2
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)
11.81.8693.60.215.144.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1K4V1.824.8431104101590.60.1820.1820.192RANDOM17.6
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]
-1.98-3.03-2.834.81
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.5
c_scangle_it1.65
c_angle_deg1.39
c_scbond_it1.09
c_mcangle_it1.06
c_improper_angle_d0.92
c_mcbond_it0.65
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.5
c_scangle_it1.65
c_angle_deg1.39
c_scbond_it1.09
c_mcangle_it1.06
c_improper_angle_d0.92
c_mcbond_it0.65
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2315
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms27

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing