5NPR | pdb_00005npr

The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PE4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	295	Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4

Crystal Properties
Matthews coefficient	Solvent content
3.33	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.038	α = 90
b = 150.951	β = 90
c = 200.54	γ = 90

Symmetry
Space Group	F 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	46.01	99.5	0.06	0.078	0.048	0.99	9.7	4		88158

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	99.8		0.871	1.202	0.711	0.65	1.3	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3PE4	1.85	46.01	83781	4369	99.42	0.2065	0.20497	0.22	0.23641	0.26	RANDOM	46.58

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]
-2.79			4.54		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.605
r_dihedral_angle_4_deg	18.311
r_dihedral_angle_3_deg	13.492
r_long_range_B_refined	6.534
r_long_range_B_other	6.466
r_dihedral_angle_1_deg	6.026
r_scangle_other	4.74
r_mcangle_other	3.723
r_mcangle_it	3.721
r_scbond_it	2.912
r_scbond_other	2.912
r_mcbond_it	2.499
r_mcbond_other	2.498
r_angle_refined_deg	1.408
r_angle_other_deg	0.968
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5564
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building