4DFL | pdb_00004dfl

Crystal structure of spleen tyrosine kinase complexed with a sulfonamidopyrazine piperidine inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.028	α = 90
b = 85.004	β = 90
c = 90.748	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	PILATUS 6M	DECTRIS			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	62.02	99.6	0.05		8		22265

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.04	98.4		0.764		8.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	THROUGHOUT	NONE	1.98	62.02	22265	20689	1483	99.59	0.19921	0.19616	0.2	0.24304	0.25	RANDOM	49.82

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]
0.21			-2.44		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.152
r_dihedral_angle_4_deg	17.253
r_dihedral_angle_3_deg	12.404
r_dihedral_angle_1_deg	5.297
r_scangle_it	3.591
r_scbond_it	2.756
r_mcangle_it	1.865
r_mcbond_it	1.515
r_angle_refined_deg	1.127
r_angle_other_deg	0.747
r_mcbond_other	0.314
r_symmetry_hbond_refined	0.279
r_symmetry_vdw_other	0.22
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.197
r_nbtor_refined	0.181
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.126
r_nbtor_other	0.083
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2140
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling