3TD6 | pdb_00003td6

Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis from trigonal partially dehydrated crystal

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z2I	PDB ENTRY 2Z2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	7.5	291	0.1M HEPES, 25% PEG 8000, 5% dioxane, pH 7.5, Microbatch under oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2	38.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.47	α = 90
b = 59.47	β = 90
c = 80.42	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	MAR scanner 345 mm plate	Mirrors	2010-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	3.2	43		0.155	9.9	3.9		2900			32.3

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	3.2	3.37

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 2Z2I	3.2	30	2750	132	98.36	0.23347	0.23172	0.23	0.2698	0.27	RANDOM	18.918

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]
-1.8	-0.9		-1.8		2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.161
r_dihedral_angle_3_deg	22.106
r_dihedral_angle_4_deg	19.992
r_mcangle_it	15.651
r_mcbond_it	11.682
r_dihedral_angle_1_deg	4.679
r_angle_refined_deg	1.526
r_scangle_it	0.489
r_scbond_it	0.435
r_symmetry_hbond_refined	0.372

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.161
r_dihedral_angle_3_deg	22.106
r_dihedral_angle_4_deg	19.992
r_mcangle_it	15.651
r_mcbond_it	11.682
r_dihedral_angle_1_deg	4.679
r_angle_refined_deg	1.526
r_scangle_it	0.489
r_scbond_it	0.435
r_symmetry_hbond_refined	0.372
r_symmetry_vdw_refined	0.33
r_nbtor_refined	0.327
r_nbd_refined	0.285
r_xyhbond_nbd_refined	0.209
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1340
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.