8P0L

Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.499	α = 90
b = 101.499	β = 90
c = 284.617	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 EIGER2 XE 9M		2018-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.5	284.62	100	0.101	0.108	0.037	0.999	14.4	15.7		52629

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.58			0.84	0.892	0.3	0.843		16.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	95.785	52525	1571	99.964	0.218	0.2158	0.2711	68.096

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]
-4.059			-4.059		8.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.029
r_dihedral_angle_6_deg	16.378
r_lrange_other	11.633
r_lrange_it	11.632
r_dihedral_angle_2_deg	11.39
r_mcangle_it	10.176
r_mcangle_other	10.175
r_scangle_it	8.962
r_scangle_other	8.962
r_dihedral_angle_1_deg	7.496
r_mcbond_it	6.952
r_mcbond_other	6.948
r_scbond_it	6.343
r_scbond_other	6.342
r_angle_refined_deg	1.446
r_symmetry_xyhbond_nbd_refined	0.566
r_angle_other_deg	0.504
r_nbd_other	0.282
r_nbd_refined	0.241
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.196
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_other	0.117
r_dihedral_angle_other_3_deg	0.086
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.066
r_chiral_restr_other	0.044
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6955
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling