2RKJ | pdb_00002rkj

Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y42	PDB ENTRIES 1Y42, 1Y0Q
experimental model	PDB	1Y0Q	PDB ENTRIES 1Y42, 1Y0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1M cacodylate, 1.8 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.92	75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 231.063	α = 90
b = 123.525	β = 90.26
c = 235.231	γ = 90

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD		2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97918	APS	23-ID-D

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	4.5	50	82.8	0.094	11	3	79214	66194

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)
	4.5	4.66	42.5		0.394	1.86	1.9	3375

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-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 ENTRIES 1Y42, 1Y0Q	4.5	47.88	79214	66048	3330	83.3	0.235	0.2349	0.249	0.25	RANDOM	211.9

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]
-7.54		-0.31	12.64		-5.1

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.5
c_scangle_it	1.97
c_mcangle_it	1.63
c_improper_angle_d	1.35
c_angle_deg	1.2
c_scbond_it	1.18
c_mcbond_it	0.92
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23616
Nucleic Acid Atoms	20720
Solvent Atoms
Heterogen Atoms

Software

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