5D7V | pdb_00005d7v

Crystal structure of PTK6 kinase domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.23M Diammonium Phosphate, 18% PEG 3350, 1M Lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.718	α = 81.46
b = 76.308	β = 75.92
c = 87.271	γ = 74.93

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	IMAGE PLATE	MAR scanner 345 mm plate	VariMax HR	2015-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54789

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	2.33	50	96.3	0.113	7.3	2.1		50742

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	2.33	2.41	94.2		0.443	1.9	2.1

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	2F4J	2.33	50	46364	2476	95.98	0.2218	0.2186	0.2183	0.2816	0.2794	RANDOM	26.633

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]
1.67	-0.49	0.87	-0.61	-0.29	-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.401
r_dihedral_angle_3_deg	17.169
r_dihedral_angle_4_deg	16.644
r_dihedral_angle_1_deg	5.813
r_scangle_it	1.491
r_angle_refined_deg	1.175
r_scbond_it	0.922
r_mcangle_it	0.689
r_mcbond_it	0.387
r_nbtor_refined	0.295
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8592
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	92

Software

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