5E9E | pdb_00005e9e

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	20% PEG8000, 0.1 M MOPS, 0.2 M magnesium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.601	α = 90
b = 110.112	β = 90
c = 78.265	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 210		2007-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.979	CHESS	F2

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	30	97.7	0.123	23.53	4.2	28601	28345			38.4

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	86.1		0.349		3.1

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	PDB entry 3LMH	2.4	30	26910	1434	99.1	0.1936	0.1913	0.2	0.2359	0.24	RANDOM	42.823

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]
-2.82			0.96		1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.285
r_dihedral_angle_4_deg	21.921
r_dihedral_angle_3_deg	13.315
r_dihedral_angle_1_deg	6.419
r_mcangle_it	4.499
r_mcbond_it	2.753
r_mcbond_other	2.753
r_angle_refined_deg	1.491
r_angle_other_deg	0.947
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.285
r_dihedral_angle_4_deg	21.921
r_dihedral_angle_3_deg	13.315
r_dihedral_angle_1_deg	6.419
r_mcangle_it	4.499
r_mcbond_it	2.753
r_mcbond_other	2.753
r_angle_refined_deg	1.491
r_angle_other_deg	0.947
r_chiral_restr	0.078
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	4078
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	74

Software

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

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.