5OXD | pdb_00005oxd

Complex of a C. perfringens O-GlcNAcase with a fragment hit

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Apo crystals were grown in 0.6 M NaAcetate pH 7.5, 0.175 M cadmium sulphate (ML). Crystals were then transferred into a drop supplemented with 10 mM ligand and incubated for 4 h. Crystals were cryo-protected by short immersion in ML supplemented with 20% glycerol and saturated with ligand.

Crystal Properties
Matthews coefficient	Solvent content
4.46	72.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.794	α = 90
b = 117.794	β = 90
c = 147.233	γ = 120

Symmetry
Space Group	P 61

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 EIGER X 4M		2017-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9678	ESRF	MASSIF-3

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	2.6	50.01	99.1	0.222	0.254	0.122	0.993	7.9	7.9		35270

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	2.6	2.72	99.5		2.38	2.704	0.1273	0.7	1	8.2

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	2YDS	2.6	50.01	33390	1880	99.06	0.17436	0.17174	0.18	0.22061	0.22	RANDOM	62.48

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]
2.15	1.07		2.15		-6.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.134
r_dihedral_angle_4_deg	17.58
r_dihedral_angle_3_deg	17.532
r_long_range_B_refined	10.522
r_long_range_B_other	10.522
r_scangle_other	8.657
r_dihedral_angle_1_deg	7.113
r_mcangle_it	6.492
r_mcangle_other	6.491
r_scbond_it	5.691
r_scbond_other	5.69
r_mcbond_it	4.503
r_mcbond_other	4.502
r_angle_refined_deg	1.774
r_angle_other_deg	1.085
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
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	4586
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	33

Software

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