3KO3 | pdb_00003ko3

D-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomplex with ADP, obtained through soaking native enzyme crystal with the ATP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG 3350, 0.1M MES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.786	α = 72.52
b = 53.241	β = 77.85
c = 91.793	γ = 88.92

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD		2007-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	2.6	25	95.9	0.092	5.6	2.2		27620

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)
	2.6	2.69	82.2		0.481		2	2388

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	25	19900	2215	98.49	0.188	0.179	0.18	0.266	0.28	RANDOM	35.355

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]
1.16	-2.15	-1.93	-1.11	1.75	-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.806
r_dihedral_angle_3_deg	19.257
r_dihedral_angle_4_deg	17.206
r_dihedral_angle_1_deg	6.966
r_scangle_it	2.02
r_angle_refined_deg	1.442
r_scbond_it	1.226
r_mcangle_it	1.122
r_mcbond_it	0.621
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.806
r_dihedral_angle_3_deg	19.257
r_dihedral_angle_4_deg	17.206
r_dihedral_angle_1_deg	6.966
r_scangle_it	2.02
r_angle_refined_deg	1.442
r_scbond_it	1.226
r_mcangle_it	1.122
r_mcbond_it	0.621
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.275
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.223
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7630
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	27

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.