3S95 | pdb_00003s95

Crystal structure of the human LIMK1 kinase domain in complex with staurosporine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YI6	PDB ENTRY 1YI6 and 2QO9
experimental model	PDB	2QO9	PDB ENTRY 1YI6 and 2QO9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293.15	24% MPD, 0.1M Tris pH 7.2, 10mM Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.16	α = 90
b = 128	β = 90
c = 131.35	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	PSI PILATUS 6M		2011-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.65	43.78	98.7	0.068	11	4.1	105650	105524			21.6

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	1.65	1.74	98.5		0.608	2.2	4.1	15293

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YI6 and 2QO9	1.65	40.86	2	105524	100253	5270	98.39	0.15673	0.15544	0.1611	0.18084	0.1846	RANDOM	24.827

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]
1.14			-0.04		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.038
r_dihedral_angle_4_deg	17.048
r_dihedral_angle_3_deg	13.741
r_scangle_it	9.704
r_scbond_it	7.013
r_dihedral_angle_1_deg	5.887
r_mcangle_it	4.85
r_mcbond_it	3.002
r_angle_refined_deg	1.557
r_angle_other_deg	0.987
r_mcbond_other	0.854
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4647
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	164

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling