8J2W

Saccharothrix syringae photocobilins protein, dark state

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	38% v/v 1,4-Dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.111	α = 90
b = 97.539	β = 116.72
c = 72.662	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2022-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.7	75.18	99.8	0.083	1	15	6.9		90363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	95.9		0.953	0.7	1.1	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	75.18	85824	4537	99.79	0.1843	0.18286	0.21176	RANDOM	34.958

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]
-0.09		0.07	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.739
r_long_range_B_refined	6.949
r_long_range_B_other	6.899
r_dihedral_angle_1_deg	6.719
r_scangle_other	4.741
r_scbond_it	3.394
r_scbond_other	3.393
r_mcangle_it	3.306
r_mcangle_other	3.306
r_dihedral_angle_2_deg	2.863
r_mcbond_it	2.386
r_mcbond_other	2.386
r_angle_refined_deg	1.622
r_angle_other_deg	0.494
r_chiral_restr	0.14
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4955
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	336

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
PHASER	phasing