4ZME | pdb_00004zme

Crystal Structure of the Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A in Complex with Adenosine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LKM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	277.15	PEG 8000, sodium phosphate, cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.194	α = 90
b = 111.288	β = 90
c = 79.56	γ = 90

Symmetry
Space Group	P 21 21 2

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	White beam collimating mirror	2007-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.918	CHESS	F1

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	1.98	79.56	99.5	0.09	6.9	6.9		51052			29.2

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	1.98	2.07	99.9		0.43	6.45	4.7

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	3LKM	1.98	79.56	46516	2480	94.28	0.2148	0.2136	0.22	0.2361	0.24	RANDOM	37.036

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]
-1.72			1.25		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.632
r_dihedral_angle_4_deg	17.769
r_dihedral_angle_3_deg	13.848
r_dihedral_angle_1_deg	6.48
r_mcangle_it	3.768
r_mcbond_other	2.393
r_mcbond_it	2.392
r_angle_refined_deg	1.49
r_angle_other_deg	0.942
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.632
r_dihedral_angle_4_deg	17.769
r_dihedral_angle_3_deg	13.848
r_dihedral_angle_1_deg	6.48
r_mcangle_it	3.768
r_mcbond_other	2.393
r_mcbond_it	2.392
r_angle_refined_deg	1.49
r_angle_other_deg	0.942
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4079
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	70

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.