3NEA | pdb_00003nea

Crystal Structure of Peptidyl-tRNA hydrolase from Francisella tularensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PTH	PDB ENTRY 2PTH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	25% PEG3350, 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.683	α = 90
b = 93.043	β = 90
c = 33.027	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HR	2007-08-28	M	SINGLE WAVELENGTH
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.25	50	100	0.14	6	6.6		9412

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)
1	2.25	2.33	100		0.49		6.7	906

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2PTH	2.25	33.03	9380	438	99.97	0.193	0.19	0.1937	0.248	0.2498	RANDOM	25.057

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]
-0.37			-0.11		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.208
r_dihedral_angle_4_deg	21.475
r_dihedral_angle_3_deg	16.728
r_dihedral_angle_1_deg	5.863
r_scangle_it	2.916
r_scbond_it	1.794
r_angle_refined_deg	1.291
r_mcangle_it	1.096
r_mcbond_it	0.575
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1450
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	21

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling