7L6L | pdb_00007l6l

Crystal Structure of the DNA-binding Transcriptional Repressor DeoR from Escherichia coli str. K-12

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	Protein: 3.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Glycerol, TEV; Screen: Classics II (G5), 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.751	α = 90
b = 64.734	β = 97.94
c = 140.71	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD	Be	2019-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	30	99.8	0.07	0.07	0.079	0.036	24	4.8		127632		-3	24.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	99.4		0.781	0.781	0.876	0.393	0.814	2.3	4.8

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	SAD	THROUGHOUT	1.75	29.7	120563	6304	99.71	0.1593	0.158	0.17	0.1832	0.19	RANDOM	28.471

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]
1.61		1.71	-0.71		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.728
r_dihedral_angle_3_deg	9.039
r_dihedral_angle_4_deg	7.332
r_dihedral_angle_1_deg	3.481
r_angle_refined_deg	1.346
r_angle_other_deg	0.371
r_chiral_restr	0.063
r_gen_planes_refined	0.052
r_gen_planes_other	0.047
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.728
r_dihedral_angle_3_deg	9.039
r_dihedral_angle_4_deg	7.332
r_dihedral_angle_1_deg	3.481
r_angle_refined_deg	1.346
r_angle_other_deg	0.371
r_chiral_restr	0.063
r_gen_planes_refined	0.052
r_gen_planes_other	0.047
r_bond_refined_d	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8583
Nucleic Acid Atoms
Solvent Atoms	1309
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.