357D

3.5 A structure of fragment I from E. coli 5S RRNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.4		pH 6.40, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.14	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.67	α = 90
b = 58.67	β = 90
c = 248.84	γ = 120

Symmetry
Space Group	P 61 2 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	IMAGE PLATE	FUJI	SILICON 111 BENDING MIRROR	1996-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

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	3.5	20	99.1	0.057	0.057	11.3	4.9		6037	-3	-3	56.6

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)
	3.5	3.62	95.1		0.291	0.291	3.7	4.5

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD PHASES FROM A BROMINE WERE COMBINED WITH MAD AND SIRAS PHASES FROM A MERCURY DERIVIATIVE. MLPHARE WAS USED TO CALCULATE THE PHASES WHILE SIGMAA WAS USED TO COMBINE THE THREE PHASES SETS.	THROUGHOUT	3.5	10	3374	372	97.4	0.312	0.312	0.265	RANDOM	98.6

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]
6.05	32.87		6.05		-12

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	29.9
c_improper_angle_d	2.63
c_mcangle_it	2.34
c_scangle_it	1.64
c_angle_deg	1.5
c_mcbond_it	1.35
c_scbond_it	0.98
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1294
Solvent Atoms
Heterogen Atoms	9

Software

Software
Software Name	Purpose
CCP4	model building
X-PLOR/CNS	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing
X-PLOR	phasing
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.