6WN5 | pdb_00006wn5

1.52 Angstrom Resolution Crystal Structure of Transcriptional Regulator HdfR from Klebsiella pneumoniae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 7.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen (PACT, E10): 0.2 M Sodium/Potassium phosphate, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.389	α = 90
b = 62.389	β = 90
c = 103.132	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	CCD	MARMOSAIC 300 mm CCD	Be	2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.52	30	100	0.057	0.057	0.061	0.019	44.4	9.5		32133		-3	22.2

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	1.52	1.55	100		0.783	0.783	0.827	0.263	0.91	3.4	9.5

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	1.52	29.86	30411	1656	99.94	0.1833	0.1821	0.19	0.2049	0.22	RANDOM	26.801

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]
0.67			0.67		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.971
r_dihedral_angle_4_deg	16.051
r_dihedral_angle_3_deg	10.813
r_dihedral_angle_1_deg	5.341
r_angle_refined_deg	1.499
r_angle_other_deg	0.405
r_chiral_restr	0.069
r_gen_planes_refined	0.055
r_gen_planes_other	0.05
r_bond_refined_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.971
r_dihedral_angle_4_deg	16.051
r_dihedral_angle_3_deg	10.813
r_dihedral_angle_1_deg	5.341
r_angle_refined_deg	1.499
r_angle_other_deg	0.405
r_chiral_restr	0.069
r_gen_planes_refined	0.055
r_gen_planes_other	0.05
r_bond_refined_d	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1399
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	3

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.