5M7U

Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2920.1-0.2 M tri Ammonium citrate pH 7.5 16-20 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4750.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.23α = 90
b = 101.23β = 90
c = 284.673γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.395.561000.0820.99617.813.266853
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.351002.6970.581.213.6

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5m7r2.395.5666741199199.950.20090.20010.2274RANDOM80.1799
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]
-1.44-1.442.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg16.619
r_dihedral_angle_1_deg6.186
r_angle_other_deg3.625
r_mcangle_it2.758
r_mcbond_it1.741
r_mcbond_other1.741
r_angle_refined_deg1.562
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg16.619
r_dihedral_angle_1_deg6.186
r_angle_other_deg3.625
r_mcangle_it2.758
r_mcbond_it1.741
r_mcbond_other1.741
r_angle_refined_deg1.562
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_other0.01
r_gen_planes_refined0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7334
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing