3E9D | pdb_00003e9d

Structure of full-length TIGAR from Danio rerio

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	1 M sodium phosphate, pH 6.5, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.661	α = 90
b = 115.541	β = 104.66
c = 61.311	γ = 90

Symmetry
Space Group	C 1 2 1

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			2008-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.979	NSLS	X4C

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	30	96.1	0.076		3		57061

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	79.3		0.425		2.2	4700

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	30	56186	2835	96.88	0.173	0.171	0.1716	0.213	0.2147	RANDOM	28.07

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]
1.63		-0.32	-0.7		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.786
r_dihedral_angle_4_deg	14.38
r_dihedral_angle_3_deg	12.796
r_dihedral_angle_1_deg	5.526
r_scangle_it	3.613
r_scbond_it	2.163
r_mcangle_it	1.406
r_angle_refined_deg	1.14
r_mcbond_it	0.736
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3826
Nucleic Acid Atoms
Solvent Atoms	698
Heterogen Atoms	22

Software

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