6T8Q | pdb_00006t8q

HKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)-7-oxo-6H,7H-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]pyrrolidine-2-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TF5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 400, cadmium chloride, sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
4.39	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.829	α = 90
b = 144.829	β = 90
c = 139.653	γ = 120

Symmetry
Space Group	P 65 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		2017-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.51	125.43	95.9	0.05	0.107	0.995	10.63	4.3		28843			30.166

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.51	2.76	97.2		0.431	0.023	0.999	46.86	4.2

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	5TF5	2.51	125.43	27915	928	95.86	0.1795	0.1783	0.183	0.2162	0.2208	RANDOM	56.36

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]
0.6	0.3		0.6		-1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.202
r_dihedral_angle_4_deg	16.421
r_dihedral_angle_3_deg	13.599
r_dihedral_angle_1_deg	7.087
r_angle_refined_deg	1.673
r_angle_other_deg	1.296
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3369
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	45

Software

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