12FJ | pdb_000012fj

Crystal structure of 6-fluoropyrazolo[1,5-a]pyridine derivative bound to KIT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		proprietary

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.75	293	PEG 6K, BICINE

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.338	α = 90
b = 78.537	β = 90
c = 94.494	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X CdTe 16M		2023-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8856	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.629	60.399	100	0.1103	0.1188	0.0433	0.996	8.07	7.63		10528

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.629	2.675	100		2.0175	2.1642	0.7736	0.288	1.27	7.9

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	2.629	60.399	10519	514	99.915	0.25	0.2462	0.2492	0.3202	0.3179	75.851

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]
-1.128			1.386		-0.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.057
r_dihedral_angle_other_6_deg	22.791
r_dihedral_angle_4_deg	16.583
r_dihedral_angle_3_deg	14.34
r_dihedral_angle_6_deg	10.04
r_lrange_it	8.079
r_lrange_other	8.078
r_dihedral_angle_1_deg	6.557
r_mcangle_it	5.727
r_mcangle_other	5.725
r_scangle_it	5.035
r_scangle_other	5.034
r_mcbond_it	3.577
r_mcbond_other	3.576
r_scbond_it	3.056
r_scbond_other	3.054
r_angle_refined_deg	1.319
r_angle_other_deg	1.104
r_nbd_refined	0.156
r_nbtor_refined	0.151
r_symmetry_nbd_other	0.146
r_nbd_other	0.133
r_xyhbond_nbd_refined	0.091
r_symmetry_xyhbond_nbd_refined	0.077
r_symmetry_nbtor_other	0.072
r_symmetry_nbd_refined	0.056
r_chiral_restr	0.048
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2477
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	29

Software

Software
Software Name	Purpose
autoPROC	data processing
Aimless	data scaling
TRUNCATE	data processing
REFMAC	refinement
XDS	data reduction
REFMAC	phasing