4KHP

Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	100 mM Mes-KOH (pH 6.5), 200 mM KCl, 75 mM NH4Cl, 15 mM MgCl2, and 26% (vol/vol) 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
4.64	73.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 401	α = 90
b = 401	β = 90
c = 176	γ = 90

Symmetry
Space Group	P 41 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.99	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	29.7	91.4			234683	234683

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.2	95.1		0.691	1.47

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 15JE	3.1	29.67	234682	234682	11726	91.35	0.1873	0.1873	0.1852	0.2262	RANDOM	83.2593

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.871
r_dihedral_angle_3_deg	23.112
r_dihedral_angle_4_deg	20.012
r_mcangle_it	10.609
r_dihedral_angle_1_deg	8.601
r_mcbond_it	6.718
r_mcbond_other	6.718
r_angle_refined_deg	1.751
r_angle_other_deg	1.26
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.871
r_dihedral_angle_3_deg	23.112
r_dihedral_angle_4_deg	20.012
r_mcangle_it	10.609
r_dihedral_angle_1_deg	8.601
r_mcbond_it	6.718
r_mcbond_other	6.718
r_angle_refined_deg	1.751
r_angle_other_deg	1.26
r_chiral_restr	0.101
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19120
Nucleic Acid Atoms	32485
Solvent Atoms
Heterogen Atoms	427

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

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.