2ZNJ

Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		PylS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	50mM Na cacodylate, 50mM Ammonium sulfate, 20% PEG400, 10mM Na acetate, 0.2mM Na formate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.925	α = 90
b = 128.555	β = 90
c = 124.241	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315	mirrors	2007-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.5	50	100	0.076	55.82	14.5	35020	35020			32.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PylS	2.5	44.67	34900	1768	100	0.214	0.214	0.275	RANDOM	40.2

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]
-7.64			-4.92		12.55

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_scangle_it	2.57
c_mcangle_it	2.31
c_scbond_it	1.61
c_mcbond_it	1.32
c_angle_deg	1.3
c_improper_angle_d	0.78
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6773
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing