9Y5A | pdb_00009y5a

Co-crystal structure of BTK kinase domain with non-covalent inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6X3N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10% PEG 20000, 20% PEG MME 550, 0.03 M Sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, and 0.1 M MES/Imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.527	α = 90
b = 104.615	β = 90
c = 37.908	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 16M		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	50	88	0.074	0.997	25.4	7.3		32367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63			0.848	0.63

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	42.258	30092	1487	93.578	0.145	0.1429	0.1576	0.1752	0.1858	16.983

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]
0.095			0.225		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.119
r_dihedral_angle_3_deg	15.036
r_dihedral_angle_6_deg	14.719
r_lrange_it	7.777
r_lrange_other	7.572
r_dihedral_angle_other_2_deg	6.912
r_dihedral_angle_1_deg	6.892
r_scangle_it	5.051
r_scangle_other	5.05
r_mcangle_it	3.262
r_mcangle_other	3.262
r_scbond_it	3.196
r_scbond_other	3.195
r_mcbond_it	2.067
r_mcbond_other	2.066
r_angle_refined_deg	1.879
r_angle_other_deg	0.647
r_symmetry_nbd_refined	0.294
r_symmetry_xyhbond_nbd_refined	0.287
r_nbd_other	0.248
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.235
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.186
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing