5MG1 | pdb_00005mg1

Structure of the photosensory module of Deinococcus phytochrome by serial femtosecond X-ray crystallography

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O9C	PAS-GAF from PDB 2O9C, and PHY domain from 4Q0J
experimental model	PDB	4Q0J	PAS-GAF from PDB 2O9C, and PHY domain from 4Q0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	298	PEG 3350, Tacsimate pH 6.0, Tacsimate pH 7.0, ethylene glycol, PIPES-NaOH pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.43	72.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.7	α = 90
b = 151.7	β = 90
c = 151.2	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	RAYONIX MX170-HS	Compound refractive lenses	2015-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.305	SLAC LCLS	MFX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.3	131.376	99.86	0.863	29.234	39.16		15996

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	3.3	3.3569	99.87		0.178	4.069	20.75

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PAS-GAF from PDB 2O9C, and PHY domain from 4Q0J	3.3	37.894	1.34	15968	820	99.94	0.2135	0.2117	0.21	0.2447	0.24	91.6934

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.379
f_angle_d	0.562
f_chiral_restr	0.038
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3726
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	43

Software

Software
Software Name	Purpose
cctbx.xfel	data collection
cctbx.prime	data reduction
cctbx.xfel	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
psana	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.