9Y56 | pdb_00009y56

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

X-RAY DIFFRACTION

---

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
2.21	44.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.024	α = 90
b = 104.334	β = 90
c = 37.921	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		2022-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9794	APS	21-ID-D

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	95.9	0.117	0.994	24.8	7.3		36963

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	1.601	1.643			0.783

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	1.601	42.285	36466	1810	94.673	0.154	0.1522	0.152	0.1855	0.1883	15.201

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]
-0.096			0.364		-0.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.011
r_dihedral_angle_6_deg	15.542
r_dihedral_angle_3_deg	11.987
r_lrange_it	7.319
r_dihedral_angle_1_deg	7.134
r_lrange_other	6.827
r_scangle_it	4.7
r_scangle_other	4.699
r_mcangle_other	3.206
r_mcangle_it	3.203
r_scbond_it	3.096
r_scbond_other	3.095
r_mcbond_it	2.016
r_mcbond_other	2.016
r_angle_refined_deg	1.942
r_dihedral_angle_other_2_deg	1.79
r_angle_other_deg	0.64
r_xyhbond_nbd_refined	0.227
r_nbd_refined	0.225
r_nbd_other	0.198
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.172
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	53

Software

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