4GFQ | pdb_00004gfq

2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EK8	PDB ENTRY 1EK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	protein: 7.4 mg/mL in 0.25 M sodium cloride, 0.01 M Tris-HCl, pH 8.3, screen: Classics II (H3), 0.24 M sodium malonate, pH 7.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.548	α = 90
b = 95.548	β = 90
c = 95.548	γ = 90

Symmetry
Space Group	P 2 3

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	MARMOSAIC 300 mm CCD	mirrors	2012-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07806	APS	21-ID-D

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	2.65	30	99.3	0.061	18	4.3	8662	8662		-3	87.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	100		0.553	2.5	4.4	430

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EK8	2.65	28.81	7596	7596	379	91.73	0.2051	0.2051	0.20264	0.21	0.25452	0.25	RANDOM	66.329

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.768
r_dihedral_angle_4_deg	14.231
r_dihedral_angle_3_deg	11.025
r_scangle_it	5.903
r_scbond_it	3.517
r_mcangle_it	2.005
r_dihedral_angle_1_deg	1.916
r_angle_refined_deg	1.412
r_mcbond_it	1.005
r_angle_other_deg	0.746

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.768
r_dihedral_angle_4_deg	14.231
r_dihedral_angle_3_deg	11.025
r_scangle_it	5.903
r_scbond_it	3.517
r_mcangle_it	2.005
r_dihedral_angle_1_deg	1.916
r_angle_refined_deg	1.412
r_mcbond_it	1.005
r_angle_other_deg	0.746
r_mcbond_other	0.243
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1458
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	26

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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 R01GM157729.