1TC5 | pdb_00001tc5

Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMAD model, which crystallized in a different space group (p21)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	PEG 200, MES, PEG3000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.479	α = 90
b = 67.465	β = 90
c = 174.41	γ = 90

Symmetry
Space Group	P 2 2 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		2003-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.91840	ALS	8.2.2

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	1.93	47.673	79.4	0.058	0.058	10.2	3.1	48352	48177		-3	21.114

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	1.93	2.02	28.6		0.238	0.238	2	2	2478

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	SeMAD model, which crystallized in a different space group (p21)	1.93	46.13	45547	45547	2487	79.09	0.20053	0.20053	0.19867	0.2084	0.2343	0.2418	RANDOM	21.081

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]
0.04					-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.759
r_scangle_it	6.166
r_scbond_it	3.809
r_mcangle_it	2.909
r_mcbond_it	1.749
r_angle_refined_deg	1.279
r_angle_other_deg	0.802
r_symmetry_vdw_other	0.308
r_nbd_other	0.251
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.127
r_nbtor_other	0.081
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.006
r_bond_other_d	0.003
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	5790
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing