3NNG | pdb_00003nng

Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR258E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K3I	PDB entry 1k3i

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under Paraffin oil	7	291	40% PEG 4000, 0.1M calcium chloride, 0.1M Bis-Tris Propane, pH 7.0, Microbatch under Paraffin oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.68	26.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.208	α = 90
b = 62.463	β = 90
c = 72.001	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 165 mm		2009-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97907	NSLS	X4C

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	2.177	50	99.9	0.088	21.8	4.3	26092	26066			25.6

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)
	2.18	2.26	100		0.215	5.7	3.9	2589

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1k3i	2.177	31.232	0.85	26014	1296	99.64	0.167	0.164	0.17	0.224	0.23	RANDOM	28.961

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]
6.176			1.281		-7.457

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.528
f_angle_d	1.026
f_chiral_restr	0.074
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2418
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
Rosetta	phasing
CNS	phasing
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.