4ZS4 | pdb_00004zs4

Crystal Structure of the Inactive Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A (D756A) Complexed with ATP

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	8.75	277.15	PEG 3350, lithium sulphate, Tris chloride

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.207	α = 90
b = 109.744	β = 90
c = 77.845	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	IMAGE PLATE	MAR scanner 300 mm plate		2011-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97938	APS	23-ID-D

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	2.4	50	99.9	0.14	17.826	7.6		28026			32.8

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	2.4	2.44	99.5		0.549	2.704	4.3	1185

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	2.4	50	26549	1411	96.98	0.1808	0.1785	0.18	0.2233	0.22	RANDOM	36.069

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]
-2.72			1.34		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.896
r_dihedral_angle_4_deg	20.765
r_dihedral_angle_3_deg	15.106
r_dihedral_angle_1_deg	6.457
r_mcangle_it	4.229
r_mcbond_it	2.491
r_mcbond_other	2.49
r_angle_refined_deg	1.541
r_angle_other_deg	0.977
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.896
r_dihedral_angle_4_deg	20.765
r_dihedral_angle_3_deg	15.106
r_dihedral_angle_1_deg	6.457
r_mcangle_it	4.229
r_mcbond_it	2.491
r_mcbond_other	2.49
r_angle_refined_deg	1.541
r_angle_other_deg	0.977
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4032
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	74

Software

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

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.