8UZ7 | pdb_00008uz7

Crystal structure of a novel triose phosphate isomerase identified on the shrimp transcriptome

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EYW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	Index kit (Hampton Research) No. 83 (0.2 M MgCl2-6H2O, 0.1 M Bis-Tris pH 6.5, 25% W/V PEG-3350, 20% PEG-400 as cryo-protectant)

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.564	α = 90
b = 84.253	β = 92.69
c = 73.739	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	100	CCD	MARMOSAIC 325 mm CCD		2016-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.181	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.7	55.45	93.1	0.07959	0.09037	0.999	13.73	6.1		91724			19.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.702	1.763			0.8205	0.9364	0.4462	2.22

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	1.7	55.45	1.34	91709	2025	93.1	0.189	0.1889	0.19	0.1909	0.19	23.01

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.2221
f_angle_d	0.8311
f_chiral_restr	0.0533
f_bond_d	0.0067
f_plane_restr	0.0049

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7548
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	7

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
XDS	data scaling
PHENIX	phasing