2C0T | pdb_00002c0t

Src family kinase Hck with bound inhibitor A-641359

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AD5	PDB ENTRY 1AD5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	CRYSTALLIZATION CONDITIONS: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-641359 [100 MM STOCK SOLUTION OF THE MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-641359 CONCENTRATION OF 1 MM. HCK/A-641359 WAS THEN MIXED WITH RESERVOIR SOLUTION (12% PEG 6000, 3% 1, 5-DIAMINOPENTANE, 20% GLYCEROL, 200 MM CA(OAC)2, 100 MM TRIS.HCL PH 8.0) AND EQUILBRATED AGAINST THE RESERVOIR SOLUTION BY VAPOR DIFFUSION (SITTING DROPS) AT 277 K.

Crystal Properties
Matthews coefficient	Solvent content
3.1	59.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.861	α = 90
b = 72.909	β = 95.87
c = 180.002	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH		2002-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	2.14	50	75.6	0.08	13.6	3		52558			38.1

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	2.14	2.22	24.7		0.25	3.3	1.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AD5	2.15	20	46145	2440	70.8	0.197	0.194	0.2	0.253	0.26	RANDOM	63.67

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]
2.99		-0.98	-0.92		-2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.255
r_dihedral_angle_4_deg	18.974
r_dihedral_angle_3_deg	17.593
r_dihedral_angle_1_deg	5.951
r_scangle_it	3.344
r_scbond_it	2.105
r_mcangle_it	1.475
r_angle_refined_deg	1.427
r_mcbond_it	0.873
r_nbtor_refined	0.307
r_nbd_refined	0.205
r_metal_ion_refined	0.186
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6925
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	90

Software

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