3MKD | pdb_00003mkd

Crystal structure of myosin-2 dictyostelium discoideum motor domain S456Y mutant in complex with adp-orthovanadate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VOM	PDB ENTRY 1VOM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	278	50mM HEPES, 140mM sodium chloride, 11%(w/v) PEG 5000, 5mM magnesium chloride, 5mM DTT, 1mM EGTA, 2%(v/v) MPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.601	α = 90
b = 147.356	β = 90
c = 153.899	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	CCD	ADSC QUANTUM 315r	bent cylindrical mirror	2008-05-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2010-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.00905	ESRF	ID23-1
2	SYNCHROTRON	BESSY BEAMLINE 14.1	1.00605	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	15	94.8	0.093	0.069	16.2	5.3	49256	49256	2	3	43.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.3	70.1		0.471	0.47	2.9	3.6	4468

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1VOM	2.4	8	38972	38972	1940	100	0.2	0.2	0.1985	0.21	0.2399	0.24	RANDOM	41.584

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]
-8.577			-0.529		9.107

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.37
c_bond_d	0.0087

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5545
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms	33

Software

Software
Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

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.