3ERR | pdb_00003err

Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SRY	pdb entry 1SRY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		300	Protein was changed into crystallization buffer (20mM K-HEPES, pH7.5, 10% w/v glycerol, 0.2mM PMSF, 1mM DTT, 4mM Mg-ATP, 0.01% Na-Azide) and concentrated to 18 mg/ml. Crystallization was carried out by setting hanging drops containing 2 ul of protein, (diluted to 13.5mg/ml with 20mM K-Hepes, pH 7.5, 10% glycerol), 0.3 ul 70% glycerol and 1.8 ul of precipitant (20% PEG 4000, 200mM Ammonium sulfate, 100mM Bis-Tris, pH 5.5) over 500ml of the same precipitant solution. Crystals appeared within one day and were of dimensions up to 200 um., VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.302	α = 90
b = 144.302	β = 90
c = 159.946	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	ADSC QUANTUM 315		2008-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.5	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.27	49.27	99.4	18.6	5.6	57296	57296	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.27	2.35	94.5		62	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1SRY	2.27	49.27	2	54226	54226	2867	99.08	0.19954	0.19702	0.22	0.24655	0.25	RANDOM	55.202

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]
-0.06	-0.03		-0.06		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.274
r_dihedral_angle_3_deg	20.453
r_dihedral_angle_4_deg	19.884
r_dihedral_angle_1_deg	6.618
r_scangle_it	4.409
r_scbond_it	2.767
r_angle_refined_deg	1.923
r_mcangle_it	1.515
r_mcbond_it	0.845
r_chiral_restr	0.135

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8420
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	46

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.