5M7S | pdb_00005m7s

Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		292	0.1-0.2 M tri ammonium citrate pH 7.5 16-20 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.908	α = 90
b = 101.908	β = 90
c = 282.799	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS3 6M		2016-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.4	96.06	100	0.121	0.035	13.4	12.6		59331

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.47	100		2.857	0.847	0.463	1	11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.4	96.06	59286	1770	99.95	0.2078	0.207	0.21	0.2322	0.23	RANDOM	78.1132

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]
-0.22			-0.22		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.415
r_dihedral_angle_4_deg	18.978
r_dihedral_angle_3_deg	18.21
r_dihedral_angle_1_deg	6.411
r_angle_other_deg	3.652
r_mcangle_it	2.169
r_angle_refined_deg	1.609
r_mcbond_it	1.267
r_mcbond_other	1.267
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.415
r_dihedral_angle_4_deg	18.978
r_dihedral_angle_3_deg	18.21
r_dihedral_angle_1_deg	6.411
r_angle_other_deg	3.652
r_mcangle_it	2.169
r_angle_refined_deg	1.609
r_mcbond_it	1.267
r_mcbond_other	1.267
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_other	0.01
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7260
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.