3M6G | pdb_00003m6g

Crystal structure of actin in complex with lobophorolide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YXQ	PDB Entry 1YXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.1M MES pH 6.0, 6% methyl ether poly(ethylene glycol) 5000, 0.1M CaCl2, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.932	α = 90
b = 86.419	β = 94.91
c = 100.868	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315	Si(111) channel cut monochromator, Toroidal focusing mirror	2009-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.97630	NSLS	X6A

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	50	97.9	0.092	11.8	4	62183	60849			27.9

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	2.07	95.3		0.424		3.8	5898

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 (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 1YXQ	2	45	62183	60817	3084	97.83	0.185	0.183	0.183	0.227	0.2256	RANDOM	23.056

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]
-0.9		-0.09	0.1		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.723
r_dihedral_angle_4_deg	17.004
r_dihedral_angle_3_deg	14.386
r_dihedral_angle_1_deg	5.36
r_scangle_it	3.338
r_scbond_it	2.057
r_angle_refined_deg	1.371
r_mcangle_it	1.241
r_mcbond_it	0.659
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5482
Nucleic Acid Atoms
Solvent Atoms	693
Heterogen Atoms	176

Software

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