2UYF | pdb_00002uyf

Single mutant F111L DntR from Burkholderia sp. strain DNT in complex with thiocyanate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1M IMIDAZOL PH 6.5 0.2M KSCN 1.2M NA ACETATE

Crystal Properties
Matthews coefficient	Solvent content
4.67	73.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.604	α = 90
b = 106.604	β = 90
c = 296.448	γ = 120

Symmetry
Space Group	P 65 2 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	ADSC CCD	TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.2	30	99.2	0.08	18.6	8.8		51204		3	39.16

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	2.2	2.32	99.2		0.53	2.7	6.1

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 1UTH	2.2	30	48457	2641	99.1	0.208	0.207	0.21	0.233	0.23	RANDOM	35.74

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]
0.75	0.38		0.75		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.864
r_dihedral_angle_4_deg	19.271
r_dihedral_angle_3_deg	17.168
r_dihedral_angle_1_deg	6.73
r_scangle_it	3.879
r_scbond_it	2.481
r_angle_refined_deg	1.862
r_mcangle_it	1.707
r_mcbond_it	0.919
r_symmetry_vdw_refined	0.442
r_nbtor_refined	0.304
r_nbd_refined	0.273
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.129
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
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	3441
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing