4WT8 | pdb_00004wt8

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		293	0.2M KSCN, 0.1M Tris-HAc pH7, 3.5-4.5%(w/v) PEG20K, 3.5- 4.5%(w/v) PEG550MME

Crystal Properties
Matthews coefficient	Solvent content
3.51	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.21	α = 90
b = 457.45	β = 90
c = 639.66	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS 2M		2013-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	3.4	49.908	98.8	0.275	0.298	0.112	8.6	6.8	841002	841002

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.58	97.9		1.302	1.302	0.608	0.5	5	121152

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		THROUGHOUT	3.4	49.908	841002	41975	98.54	0.2062	0.2044	0.2077	0.2412	0.2411	RANDOM	80.037

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]
-2.93			0.16		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.228
r_dihedral_angle_3_deg	21.499
r_dihedral_angle_4_deg	17.948
r_mcangle_it	12.446
r_dihedral_angle_1_deg	8.382
r_mcbond_it	7.605
r_mcbond_other	7.605
r_angle_refined_deg	1.615
r_angle_other_deg	1.28
r_chiral_restr	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.228
r_dihedral_angle_3_deg	21.499
r_dihedral_angle_4_deg	17.948
r_mcangle_it	12.446
r_dihedral_angle_1_deg	8.382
r_mcbond_it	7.605
r_mcbond_other	7.605
r_angle_refined_deg	1.615
r_angle_other_deg	1.28
r_chiral_restr	0.148
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19157
Nucleic Acid Atoms	32502
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
SCALA	data scaling
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.