1A04 | pdb_00001a04

THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	277	THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M TRIS.HCL (PH=8.5), 0.2 M SODIUM ACETATE, AND 30% POLYETHYLENE GLYCOL (PEG) 4000. SITTING DROPS CONTAINING 20 ML OF MIXTURE WERE EQUILIBRATED BY VAPOR DIFFUSION AT 4 DEGREES AGAINST 20 ML OF THE RESERVOIR SOLUTION. CRYSTALS BEGAN TO APPEAR AS CLUSTERS OF PLATES AFTER 11-15 DAYS., vapor diffusion - sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.306	α = 90
b = 38.527	β = 131.91
c = 106.892	γ = 90

Symmetry
Space Group	C 1 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	93	IMAGE PLATE	RIGAKU		1995-07-27	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.2	65	99.87	0.078	0.078	9.8	5.4		22871			20

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.44	99.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RNL	2.2	8	22321		99	0.211	0.211	0.2	0.267	RANDOM	20

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
x_angle_deg	1.36
x_bond_d	0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3174
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing