1N8R | pdb_00001n8r

Structure of large ribosomal subunit in complex with virginiamycin M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JJ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	292	1.2M KCl, 0.5M (NH4)Cl, 30mM MgCl2, 8% PEG, pH 5.80, VAPOR DIFFUSION, SITTING DROP at 292K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 212.902	α = 90
b = 300.474	β = 90
c = 575.176	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2000-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.0332	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	50	98.7	0.144	0.144	7.7	3.6	344322	339727		-3	33.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3	3.05	97.7		0.49	0.49	1.7	2.1	16729

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JJ2	3	20	346861	327972	3203	94.6	0.2011	0.201	0.242	same reflections as 1JJ2	43.9

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]
5.14			1.7		-6.84

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	15.6
c_scangle_it	2.02
c_mcangle_it	1.84
c_improper_angle_d	1.57
c_angle_deg	1.3
c_scbond_it	1.3
c_mcbond_it	1.12
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28801
Nucleic Acid Atoms	61617
Solvent Atoms	7882
Heterogen Atoms	269

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	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.