6T3U | pdb_00006t3u

PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K5B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.95	298	60 mM Sodium Acetate, 3.3% PEG400, 1 mM DTT, 30% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.98	α = 90
b = 116.69	β = 90
c = 117.86	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	298	CCD	MPCCD		2018-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.7712	SACLA	BL3

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	grease jet	injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1		undefined (µl/min)	undefined (µm)				Superlube

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	2.21	41.46	100	0.98	0.1059	6.1	106.11		39316

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.25	100		0.38	1.1464	0.88	34.3

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	5K5B	2.21	36.94	33150	1829	90.21	0.2317	0.2304	0.23	0.2562	0.26	RANDOM	78.626

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]
-0.33			-0.99		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.68
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_4_deg	12.454
r_dihedral_angle_1_deg	5.846
r_angle_refined_deg	1.152
r_angle_other_deg	0.899
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.68
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_4_deg	12.454
r_dihedral_angle_1_deg	5.846
r_angle_refined_deg	1.152
r_angle_other_deg	0.899
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4794
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	86

Software

Software
Software Name	Purpose
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.