8A5S | pdb_00008a5s

Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized in dark, measured illuminated.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P7N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291.15	21% (w/v) PEG 8000, 0.22 M MgCl2, 0.11 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.426	α = 90
b = 51.852	β = 90
c = 80.381	γ = 90

Symmetry
Space Group	P 21 21 21

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	Bruker PHOTON II	HELIOS optics for MetalJet	2020-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2 70 kV	1.3418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.85	43.57	99.7	0.116	0.129	0.055	0.996	10.9	5.2		16065			9.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	99.9		0.772	0.881	0.418	0.636	1.9	4.2

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 (All)	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	3P7N	1.85	40.223	16016	815	99.565	0.161	0.1613	0.1606	0.17	0.2154	0.18	Random selection	17.705

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]
0.482			-0.476		-0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.37
r_dihedral_angle_other_3_deg	23.857
r_dihedral_angle_4_deg	18.015
r_dihedral_angle_3_deg	14.785
r_lrange_it	5.808
r_dihedral_angle_1_deg	5.774
r_lrange_other	5.567
r_scangle_it	3.489
r_scangle_other	3.487
r_mcangle_it	2.481
r_mcangle_other	2.48
r_scbond_other	2.272
r_scbond_it	2.271
r_angle_other_deg	2.263
r_angle_refined_deg	1.667
r_mcbond_it	1.632
r_mcbond_other	1.631
r_nbd_refined	0.231
r_symmetry_nbd_other	0.218
r_nbd_other	0.206
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.167
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.072
r_bond_refined_d	0.037
r_bond_other_d	0.032
r_gen_planes_other	0.016
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1602
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building