1XDN | pdb_00001xdn

High resolution crystal structure of an editosome enzyme from trypanosoma brucei: RNA editing ligase 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	PEG 3350, magnesium chloride, Tris, ATP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.911	α = 90
b = 58.579	β = 100.23
c = 52.984	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 4		2003-12-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97885, 0.97899, 0.96112	APS	19-ID

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	1.1	50	86.8	0.064	0.064	33.8			95711		2	7.293

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)
1	1.1		86.8		0.064	0.064	33.8		95711

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.2	20	78835	4149	98.3	0.12923	0.12822	0.1286	0.14805	0.1455	RANDOM	9.403

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]
-0.22		0.12	-0.02		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.763
r_scangle_it	4.258
r_scbond_it	2.829
r_mcangle_it	1.915
r_angle_refined_deg	1.42
r_mcbond_it	1.192
r_angle_other_deg	0.784
r_nbd_other	0.25
r_nbd_refined	0.22
r_symmetry_vdw_other	0.217
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.169
r_symmetry_vdw_refined	0.119
r_chiral_restr	0.084
r_nbtor_other	0.084
r_gen_planes_other	0.017
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2119
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing