2CMN | pdb_00002cmn

A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	CRYSTALS OF THE MET-R206A BJFIXLH MUTANT WERE OBTAINED AT 4 DEGREES C VIA THE HANGING-DROP VAPOR-DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (0.6-1.2 MM IN 5.0 MM TRIS-HCL, PH 8.0) AND WELL SOLUTION (50 MM HEPES, 4.5 M NACL, 5% (V/) 2-METHYL-2,4-PENTANEDIOL, PH 7.5) AND INCUBATING THE DROP OVER 0.7 ML OF WELL SOLUTION.

Crystal Properties
Matthews coefficient	Solvent content
3.25	61.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.117	α = 90
b = 127.117	β = 90
c = 58.569	γ = 120

Symmetry
Space Group	H 3 2

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	CUSTOM		2003-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	2.3	27.07	99.9	0.06	36.2	7.4		8187		-3

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	2.3	2.34	100		0.74	2.9	6.3

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LSW	2.3	20	7565	611	99.9	0.197	0.195	0.19	0.22	0.22	RANDOM	41.23

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]
0.45	0.22		0.45		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.8
r_dihedral_angle_4_deg	18.68
r_dihedral_angle_3_deg	16.975
r_scangle_it	2.476
r_dihedral_angle_1_deg	2.006
r_angle_refined_deg	1.693
r_scbond_it	1.69
r_mcangle_it	1.093
r_mcbond_it	0.721
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.209
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.109
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	924
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling