Experiment: 3DSQ

Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl tRNA synthetase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q7H	PDB ENTRY 2Q7H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	1.2 M potassium sodium tartrate, 0.1 M Tris pH 8.5, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.183	α = 90
b = 68.467	β = 136.36
c = 96.288	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		CCD	MARMOSAIC 325 mm CCD		2007-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	58.1	99.6	0.069	0.096	6.7	3.6	34245	34081			20.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	100		0.253	0.343	3.9	3.7	2490

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-Factor (All)	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 2Q7H	2.1	36.32	34245	34078	1720	99.4	0.237	0.235	0.235	0.2354	0.283	0.2822	RANDOM	39.8

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]
-9.39		-2.45	-12.02		21.42

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22
c_angle_deg	1.3
c_improper_angle_d	0.79
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4543
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	2

Software

Software
Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing