3NRL | pdb_00003nrl

Crystal Structure of protein RUMGNA_01417 from Ruminococcus gnavus, Northeast Structural Genomics Consortium Target UgR76

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Cacodylate Acid (pH 6.5), 18% PEG3350, and 0.2M ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.581	α = 90
b = 53.072	β = 90
c = 76.477	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	mirrors	2010-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97915	NSLS	X4C

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	1.9	50	98.4	0.059	0.045	29	4.3	25141	24739			10.8

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)
	1.9	1.93	91.2		0.365	0.301	3.1	3.7	1245

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	1.9	32.24	2	1245	21676	2081	86.2	0.22	0.219	0.218	0.24	0.263	0.28	RANDOM	30.113

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]
1.39			5.21		-6.6

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	9.02
c_scbond_it	6.76
c_mcangle_it	5.12
c_mcbond_it	3.98

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1140
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	10

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
REFMAC	refinement

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.