6GCV | pdb_00006gcv

Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7.5	293	Capillary counterdiffusion method: C23: 0.82 M K-phosphate, 0.82 M Na-phosphate, 0.1 M Na-Hepes pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.777	α = 90
b = 87.949	β = 93.05
c = 52.896	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	100	PIXEL	DECTRIS PILATUS 6M-F	Toroidal Mirror	2017-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.3	46.32	85.43	0.0316	0.039	0.023	0.999	14.98	2.7		88758			17.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.35	92.43		0.3744	0.4657	0.2746	0.837	2.38	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	AB INITIO PHASING	THROUGHOUT	1.3	46.32	84383	4375	85.44	0.12673	0.12535	0.14	0.15325	0.16	RANDOM	23.273

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]
-0.28		-0.14	0.11		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.287
r_sphericity_free	24.243
r_dihedral_angle_4_deg	15.866
r_dihedral_angle_3_deg	13.433
r_sphericity_bonded	11.515
r_dihedral_angle_1_deg	4.163
r_long_range_B_refined	3.359
r_long_range_B_other	3.285
r_scangle_other	2.608
r_mcangle_it	2.129
r_mcangle_other	2.129
r_rigid_bond_restr	2.114
r_scbond_it	1.984
r_scbond_other	1.984
r_mcbond_it	1.642
r_mcbond_other	1.624
r_angle_refined_deg	1.4
r_angle_other_deg	0.796
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2830
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	32

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
Arcimboldo	phasing