6GYG | pdb_00006gyg

X-ray structure of the apo form of the establishement gene regulator Reg576 of the G+ plasmid p576

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		fragments

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		300	Protein was concentrated to 25 mg/mL in [20 mM Tris (pH8.0), 250 mM NaCl]. Crystals of Reg576 were obtained in 130 mM potassium bromide, 25% PEG 2000 monomethylether by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). Needle-shaped crystals appeared in less t han a week. Cryo-cooling in liquid nitrogen was carried out using a cryo-protecting solution containing reservoir solution supplemented with 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.278	α = 90
b = 44.278	β = 90
c = 141.166	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS PILATUS 6M	KB mirrors	2017-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9789	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.979	42.25	92.6	0.106	0.999	12.5	11.6		8828			47.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.979	2.013	41.9		1.959	0.502	1.4	12.3

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	fragments	1.98	42.25	8373	453	84.12	0.20981	0.20708	0.21	0.25596	0.26	RANDOM	54.42

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]
0.32			0.32		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.454
r_dihedral_angle_3_deg	17.6
r_dihedral_angle_4_deg	14.215
r_long_range_B_refined	8.627
r_long_range_B_other	8.612
r_scangle_other	7.022
r_dihedral_angle_1_deg	5.741
r_scbond_it	4.42
r_scbond_other	4.404
r_mcangle_it	4.266
r_mcangle_other	4.263
r_mcbond_other	3.028
r_mcbond_it	3.025
r_angle_refined_deg	1.741
r_angle_other_deg	1.058
r_chiral_restr	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1050
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms

Software

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