1YOL | pdb_00001yol

Crystal structure of Src kinase domain in complex with CGP77675

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FMK	1FMK/3LCK hybrid
experimental model	PDB	3LCK	1FMK/3LCK hybrid

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.53	α = 100.38
b = 62.95	β = 89.16
c = 72.79	γ = 89.99

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	MARRESEARCH		2002-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	2.3	20	96	0.053	9.9			29676

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)
	2.3	2.5	93.5		0.203	5.2

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FMK/3LCK hybrid	2.3	20	29675	1562	97.13	0.19585	0.19312	0.24746	RANDOM	41.462

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]
-0.44	0.43	0.25	-0.42	-0.43	0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.629
r_dihedral_angle_3_deg	16.437
r_dihedral_angle_4_deg	15.032
r_dihedral_angle_1_deg	6.046
r_scangle_it	2.55
r_angle_refined_deg	1.688
r_scbond_it	1.649
r_mcangle_it	1.318
r_mcbond_it	0.857
r_angle_other_deg	0.806
r_symmetry_vdw_other	0.3
r_symmetry_vdw_refined	0.28
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.187
r_nbd_other	0.181
r_nbtor_refined	0.179
r_mcbond_other	0.141
r_nbtor_other	0.085
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4091
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
AMoRE	phasing