3TD2

Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 5

X-RAY DIFFRACTION

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
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.31	α = 90
b = 60.31	β = 90
c = 87.67	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		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	2.5	30	99.7	0.081		3.9		6725			72.9

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	2.5	2.64

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Z2I	2.5	30	6392	320	99.66	0.23747	0.23655	0.25541	RANDOM	62.471

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]
-1.45	-0.72		-1.45		2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.119
r_dihedral_angle_3_deg	19.925
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_1_deg	3.983
r_scangle_it	2.38
r_mcangle_it	1.681
r_scbond_it	1.553
r_angle_refined_deg	1.546
r_mcbond_it	0.982
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.119
r_dihedral_angle_3_deg	19.925
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_1_deg	3.983
r_scangle_it	2.38
r_mcangle_it	1.681
r_scbond_it	1.553
r_angle_refined_deg	1.546
r_mcbond_it	0.982
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.273
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.213
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.097
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1363
Nucleic Acid Atoms
Solvent Atoms	72
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 R01GM133198.