8A5R | pdb_00008a5r

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

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 = 43.81	α = 90
b = 51.961	β = 90
c = 81.063	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	2020-02-20	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	30.975	95.6	0.07	0.078	0.035	0.998	13.2	4.6		15648			10.8

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	69.6		0.437	0.567	0.355	0.773	2.5	2.2

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	30.975	15608	800	95.316	0.161	0.1607	0.15986	0.17	0.21528	0.18	Random selection	18.205

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]
0.041			-0.524		0.482

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.949
r_dihedral_angle_4_deg	18.686
r_dihedral_angle_3_deg	15.557
r_dihedral_angle_1_deg	5.814
r_lrange_it	5.779
r_lrange_other	5.698
r_scangle_it	3.741
r_scangle_other	3.74
r_mcangle_it	2.528
r_mcangle_other	2.527
r_scbond_it	2.379
r_scbond_other	2.376
r_angle_other_deg	2.289
r_angle_refined_deg	1.727
r_mcbond_it	1.676
r_mcbond_other	1.676
r_symmetry_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.22
r_nbd_refined	0.208
r_nbd_other	0.193
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.166
r_symmetry_nbd_refined	0.165
r_symmetry_xyhbond_nbd_other	0.139
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.075
r_bond_other_d	0.033
r_gen_planes_other	0.016
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1602
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	47

Software

Software
Software Name	Purpose
PROTEUM	data collection
PROTEUM	data reduction
SADABS	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement