9Y5D | pdb_00009y5d

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	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.505	α = 90
b = 104.801	β = 90
c = 37.938	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		2022-03-07	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	1.65	50	96.2	0.106	0.992	12.6	5.6		29004

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68			0.614

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	1.655	42.302	29003	1470	83.273	0.167	0.1649	0.1775	0.2	0.2087	18.627

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]
0.321			0.142		-0.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.356
r_dihedral_angle_3_deg	14.155
r_dihedral_angle_2_deg	12.593
r_dihedral_angle_other_2_deg	8.662
r_lrange_it	7.464
r_lrange_other	7.34
r_dihedral_angle_1_deg	6.704
r_scangle_it	4.728
r_scangle_other	4.727
r_mcangle_other	3.148
r_mcangle_it	3.144
r_scbond_it	2.984
r_scbond_other	2.983
r_mcbond_it	1.998
r_mcbond_other	1.982
r_angle_refined_deg	1.847
r_angle_other_deg	0.619
r_symmetry_nbd_refined	0.294
r_symmetry_xyhbond_nbd_refined	0.28
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.209
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.186
r_nbd_other	0.184
r_chiral_restr	0.09
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2215
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	68

Software

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