3NEK | pdb_00003nek

Crystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	100mM sodium MES pH 7.0, 40% MPD, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.009	α = 90
b = 80.009	β = 90
c = 116.421	γ = 120

Symmetry
Space Group	P 31 2 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	MAR CCD 165 mm		2007-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2.5	50	99.2	0.075	0.075	7.1	4.9	15446	15322			51.47

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)
	2.5	2.59	98.8		0.59	0.59	1	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	33.15	15411	15303	785	99.3	0.247	0.246	0.25	0.277	0.25	RANDOM	55.556

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]
1.49	0.75		1.49		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.919
r_dihedral_angle_3_deg	19.787
r_dihedral_angle_4_deg	16.586
r_dihedral_angle_1_deg	5.007
r_scangle_it	2.247
r_scbond_it	1.343
r_angle_refined_deg	1.116
r_mcangle_it	0.955
r_mcbond_it	0.488
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.919
r_dihedral_angle_3_deg	19.787
r_dihedral_angle_4_deg	16.586
r_dihedral_angle_1_deg	5.007
r_scangle_it	2.247
r_scbond_it	1.343
r_angle_refined_deg	1.116
r_mcangle_it	0.955
r_mcbond_it	0.488
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3507
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building
RESOLVE	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.