3OVA | pdb_00003ova

How the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	300	20% PEG 4000, 0.2 M tri-lithium citrate, 80 mM ammonium sulfate, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.942	α = 90
b = 57.942	β = 90
c = 427.945	γ = 90

Symmetry
Space Group	P 43 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	ADSC QUANTUM 4		2007-07-20	M	SINGLE WAVELENGTH

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

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	1.98	50	87.2	0.118		8.3		46253		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.98	2.05	77

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.98	48	2	43725	2326	100	0.216	0.214	0.21	0.244	0.24	RANDOM	31.451

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.627
r_dihedral_angle_4_deg	19.781
r_dihedral_angle_3_deg	17.506
r_dihedral_angle_1_deg	5.458
r_scangle_it	2.188
r_scbond_it	1.332
r_angle_refined_deg	1.279
r_mcangle_it	0.896
r_mcbond_it	0.535
r_nbtor_refined	0.297
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	3570
Nucleic Acid Atoms	720
Solvent Atoms	219
Heterogen Atoms	49

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling