9Y5B | pdb_00009y5b

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		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	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.476	α = 90
b = 104.776	β = 90
c = 37.984	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 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	1.9	50	94.6	0.197	0.955	8.8	7.8		17604

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	1.9	1.93			0.35

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	1.904	42.289	17604	881	76.214	0.192	0.1901	0.199	0.2248	0.2308	25.169

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]
0.136			0.911		-1.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.715
r_dihedral_angle_3_deg	16.995
r_dihedral_angle_6_deg	14.369
r_dihedral_angle_1_deg	7.527
r_lrange_other	7.288
r_lrange_it	7.287
r_scangle_it	5.538
r_scangle_other	5.536
r_mcangle_it	3.725
r_mcangle_other	3.724
r_scbond_it	3.391
r_scbond_other	3.39
r_mcbond_it	2.301
r_mcbond_other	2.3
r_angle_refined_deg	1.752
r_angle_other_deg	0.607
r_symmetry_xyhbond_nbd_refined	0.279
r_chiral_restr	0.278
r_nbd_refined	0.221
r_symmetry_nbd_other	0.202
r_nbd_other	0.198
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.139
r_symmetry_nbtor_other	0.084
r_chiral_restr_other	0.035
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2210
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	40

Software

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