7DVV | pdb_00007dvv

Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DVS	7DVS, 4LLN
experimental model	PDB	4LLN	7DVS, 4LLN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25%(w/v) PEGMME 2000, 0.2 M lithium sulfate, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.973	α = 90
b = 100.973	β = 90
c = 128.989	γ = 120

Symmetry
Space Group	P 32 1 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	mirrors	2018-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.49	47.06	99.9	0.083	0.089	0.999	14.63	6.992		26423			75.503

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.65	99.4		1.769	1.911	0.562	1	7.052

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	7DVS, 4LLN	2.49	47.06	25129	1262	99.84	0.2189	0.2175	0.22	0.2463	0.25	RANDOM	86.059

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]
-1.34	-0.67		-1.34		4.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.945
r_dihedral_angle_3_deg	21.691
r_dihedral_angle_4_deg	11.82
r_dihedral_angle_1_deg	6.005
r_angle_refined_deg	1.885
r_chiral_restr	0.128
r_gen_planes_refined	0.012
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2267
Nucleic Acid Atoms	1148
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

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.