5GHV

Crystal structure of an inhibitor-bound Syk

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	278	10~20%(V/V) PEG3350, 100 MM TRIS-HCL

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.269	α = 89.99
b = 41.501	β = 90.01
c = 85.091	γ = 98.9

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 270		2010-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	1.2398	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	39.78	99.7	30.18	5.7		12408

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XG2	2.8	39.78	11722	569	91.9	0.217	0.217	0.227	RANDOM	43.35

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]
-2.25	-1.61	0.05	5.08	0.09	-2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.069
r_dihedral_angle_4_deg	15.535
r_dihedral_angle_3_deg	13.419
r_dihedral_angle_1_deg	5.615
r_long_range_B_refined	2.366
r_long_range_B_other	2.365
r_angle_refined_deg	1.565
r_mcangle_it	1.354
r_mcangle_other	1.354
r_angle_other_deg	0.877
r_scangle_other	0.844
r_mcbond_it	0.724
r_mcbond_other	0.724
r_scbond_it	0.417
r_scbond_other	0.417
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4318
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	70

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement