2O1H

Naturally occurring mutation of Humna ABO(H) Galactosyltransferase in complex with UDP: GTB/M214T_UDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291ADA, manganese chloride, ammonium sulfate, MPD, glycerol, PEG 4000,, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.6α = 90
b = 149.49β = 90
c = 79.24γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IV2006-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.67201000.05415.26.713665936659
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)
11.671.731000.2994.96.33

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 REPLACEMENTTHROUGHOUT1lz71.672034825183499.960.178350.176170.22193RANDOM22.584
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]
-0.420.72-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.763
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg6.571
r_scangle_it4.612
r_scbond_it3.118
r_mcangle_it2.058
r_angle_refined_deg1.852
r_mcbond_it1.413
r_metal_ion_refined0.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.763
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg6.571
r_scangle_it4.612
r_scbond_it3.118
r_mcangle_it2.058
r_angle_refined_deg1.852
r_mcbond_it1.413
r_metal_ion_refined0.424
r_nbtor_refined0.314
r_symmetry_hbond_refined0.222
r_nbd_refined0.217
r_xyhbond_nbd_refined0.195
r_symmetry_vdw_refined0.184
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2137
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CCP4phasing