3O2R | pdb_00003o2r

Structural flexibility in region involved in dimer formation of nuclease domain of Ribonuclase III (rnc) from Campylobacter jejuni

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N3W	PDB ENTRY 3N3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (B1), 0.1M MIB buffer pH 4.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.451	α = 90
b = 61.552	β = 90.09
c = 118.093	γ = 90

Symmetry
Space Group	P 1 21 1

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	Beryllium lenses	2010-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.25	30	99.6	0.062	16.4	3	151202	151202		-3	11

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	1.25	1.27	99.4		0.359	2.6	2.4	7499

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 3N3W	1.251	29.78	143537	143537	7589	99.58	0.13501	0.13501	0.13327	0.14	0.1683	0.16	RANDOM	11.409

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]
0.13		0.05	-0.78		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.38
r_dihedral_angle_4_deg	12.021
r_dihedral_angle_3_deg	11.452
r_scangle_it	5.145
r_dihedral_angle_1_deg	4.041
r_scbond_it	3.536
r_mcangle_it	2.3
r_mcbond_other	1.933
r_rigid_bond_restr	1.716
r_mcbond_it	1.551

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.38
r_dihedral_angle_4_deg	12.021
r_dihedral_angle_3_deg	11.452
r_scangle_it	5.145
r_dihedral_angle_1_deg	4.041
r_scbond_it	3.536
r_mcangle_it	2.3
r_mcbond_other	1.933
r_rigid_bond_restr	1.716
r_mcbond_it	1.551
r_angle_refined_deg	1.287
r_angle_other_deg	0.891
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4558
Nucleic Acid Atoms
Solvent Atoms	973
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.