3MF1 | pdb_00003mf1

Crystal structure of class II aaRS homologue (Bll0957) complexed with an analogue of glycyl adenylate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	4.6	291	PEG 4000, gycerol, pH 4.6, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.092	α = 90
b = 101.304	β = 90
c = 50.479	γ = 90

Symmetry
Space Group	P 21 21 2

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	OXFORD RUBY CCD		2009-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.54056

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	2.2	20.82	99.62	0.12	17.7372	10.04	34009	33974	2	2

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	2.32	99.39		0.55		10.08	4839

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	2.2	20.41	33974	33974	1696		0.19	0.19	0.188	0.1851	0.228	0.2211	RANDOM	27.438

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]
2.216			-5.163		2.947

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	1.02
t_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4448
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	56

Software

Software
Software Name	Purpose
SCALA	data scaling
TNT	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
REFMAC	phasing
BUSTER	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.