9Z1L | pdb_00009z1l

Structure of KIT V654A mutant with Compound 1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	285	10% 2-propanol, 100 mM Na-Citrate pH 5.0, 8% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.3	α = 90
b = 56.3	β = 90
c = 202.722	γ = 90

Symmetry
Space Group	P 43 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	103	PIXEL	DECTRIS EIGER X 16M		2025-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.54	54.25	55.7	1	12.1	25.7		27422

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	1.54	1.75			0.74

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	1.543	54.247	27422	1395	55.68	0.167	0.1646	0.1787	0.2062	0.2177	23.78

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]
0.079			0.079		-0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.939
r_dihedral_angle_3_deg	10.341
r_lrange_it	7.94
r_lrange_other	7.281
r_dihedral_angle_1_deg	6.281
r_dihedral_angle_2_deg	4.404
r_scangle_it	4.1
r_scangle_other	4.099
r_mcangle_it	3.349
r_mcangle_other	3.348
r_scbond_it	2.386
r_scbond_other	2.385
r_mcbond_it	2.014
r_mcbond_other	2.004
r_angle_refined_deg	0.985
r_angle_other_deg	0.372
r_nbd_refined	0.199
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.173
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbd_refined	0.113
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.051
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2495
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
SCALA	data scaling
REFMAC	phasing