6Y42 | pdb_00006y42

Crystal Structure of RsrR complexed to a 39 basepair DNA fragment of the rsrR promoter

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	NaCl, MgCl2, CaCl2, PEG1000, PEG3350, MES, anaerobic (in glove box)

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.37	α = 90
b = 197.37	β = 90
c = 73.19	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS EIGER X 16M		2019-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00003	SLS	X06SA

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	4.3	49.34	99.5	0.087	0.104	0.057	0.995	8.8	5.8		6038

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	4.3	4.45			2.13	2.53	0.988	0.36	0.9

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	6hsd	4.3	49.34	5671	330	98.7	0.2684	0.2668	0.27	0.3002	0.3	RANDOM	253.122

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]
2.17	1.08		2.17		-7.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.832
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_4_deg	13.098
r_dihedral_angle_1_deg	4.433
r_angle_other_deg	1.306
r_angle_refined_deg	1.107
r_chiral_restr	0.049
r_gen_planes_other	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.832
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_4_deg	13.098
r_dihedral_angle_1_deg	4.433
r_angle_other_deg	1.306
r_angle_refined_deg	1.107
r_chiral_restr	0.049
r_gen_planes_other	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2282
Nucleic Acid Atoms	1476
Solvent Atoms
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.