8B6E | pdb_00008b6e

crystal structure of the DNA-binding short chromatophore-targeted protein sCTP-23166 from Paulinella chromatophora

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		alphafold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.1 M sodium HEPES pH 7.5, 15 % (w/v) PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
1.56	21.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.887	α = 83.99
b = 30.943	β = 63.45
c = 31.188	γ = 69.84

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 16M		2021-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9200	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	29	93	0.06978	0.997	12.04	3.6		27013

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.243			0.945

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	alphafold	1.2	29	25712	1310	95.39	0.1333	0.1312	0.14	0.1763	0.18	RANDOM	19.089

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]
1.39	-0.81	-2.21	-3.17	1.51	-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.377
r_dihedral_angle_4_deg	14.958
r_dihedral_angle_3_deg	11.252
r_rigid_bond_restr	6.563
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	1.993
r_angle_other_deg	1.543
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.377
r_dihedral_angle_4_deg	14.958
r_dihedral_angle_3_deg	11.252
r_rigid_bond_restr	6.563
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	1.993
r_angle_other_deg	1.543
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	802
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
AutoProcess	data reduction
AutoProcess	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.