2ZM5

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	291	0.09M MES, 24% PEG 3350, 0.18mM Ca(OAc)2, 0.01mM tri-Sodium Citrate dihydrate pH 5.6, 2% iso-Propanol, 2% PEG 4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.2	α = 90
b = 89.4	β = 90
c = 150.8	γ = 90

Symmetry
Space Group	P 21 21 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	2006-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9791	SPring-8	BL41XU

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	2.55	50	99	0.076	0.076	21.9	7.1	39165	39165		-3	64.2

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)
	2.55	2.64	93.6		0.26	0.26	3.85	6.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.55	20	39098	39165	2753	99	0.24	0.24	0.27	RANDOM	58.87

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]
0.662			-21.578		20.916

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.64
c_scangle_it	2.537
c_mcangle_it	1.986
c_improper_angle_d	1.75
c_angle_deg	1.72
c_scbond_it	1.669
c_mcbond_it	1.17
c_bond_d	0.008
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	4800
Nucleic Acid Atoms	3046
Solvent Atoms	162
Heterogen Atoms	7

Software

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