4PZJ | pdb_00004pzj

1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	protein at 1.3 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. crystallization: The Classics II Suite (A12 (#12): 100 mM Tris pH 8.5, 3 M NaCl), VAPOR DIFFUSION, SITTING DROP, temperature 295K. Cryo condition: 25% (final) sucrose.

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.623	α = 90
b = 31.623	β = 90
c = 132.34	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	Mirror	2014-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97875	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	30	98.1	0.077	0.077	51.2	12.2	9452	9452		-3	21.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	85.7		0.496	0.496	3.42	7.7	377

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.6	28.55	8945	8945	452	98.2	0.19072	0.18955	0.2044	0.21322	0.2386	RANDOM	30.482

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]
2.19			2.19		-4.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.563
r_dihedral_angle_4_deg	17.259
r_dihedral_angle_3_deg	10.521
r_dihedral_angle_1_deg	3.439
r_angle_refined_deg	2.141
r_angle_other_deg	0.863
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.563
r_dihedral_angle_4_deg	17.259
r_dihedral_angle_3_deg	10.521
r_dihedral_angle_1_deg	3.439
r_angle_refined_deg	2.141
r_angle_other_deg	0.863
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	565
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.