4I4T | pdb_00004i4t

Crystal structure of tubulin-RB3-TTL-Zampanolide complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RYC	PDB ENTRY 3RYC, 3TIN
experimental model	PDB	3TIN	PDB ENTRY 3RYC, 3TIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	3% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.77	α = 90
b = 158.64	β = 90
c = 179.24	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	PSI PILATUS 6M		2012-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99995	SLS	X06SA

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	1.8	79.4		0.103	13.35	13.5	275149	274535			33.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99		1	13.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3RYC, 3TIN	1.8	79.32	1.99	274535	274515	13945	99.77	0.1728	0.1711	0.1684	0.2043	0.2

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]
3.1254			-0.3509		-2.1148

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.703
f_angle_d	1.179
f_chiral_restr	0.069
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17547
Nucleic Acid Atoms
Solvent Atoms	1522
Heterogen Atoms	265

Software

Software
Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling