8J2X | pdb_00008j2x

Saccharothrix syringae photocobilins protein, light 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	0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
4.68	73.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.667	α = 90
b = 109.667	β = 90
c = 98.074	γ = 120

Symmetry
Space Group	P 32 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		2022-07-08	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)	R Merge I (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	1.98	98.07	99.92	0.07186	0.074	1	20.64	20.6		47811

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.01	100		2.404	0.6	0.67

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.98	94.97	45541	2271	100	0.18394	0.18316	0.19	0.20029	0.21	RANDOM	60.837

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]
-0.21	-0.11		-0.21		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.364
r_long_range_B_refined	7.542
r_long_range_B_other	7.537
r_dihedral_angle_1_deg	6.039
r_scangle_other	4.758
r_mcangle_it	3.624
r_mcangle_other	3.623
r_scbond_it	3.156
r_scbond_other	3.155
r_mcbond_it	2.405
r_mcbond_other	2.405
r_dihedral_angle_2_deg	1.745
r_angle_refined_deg	1.551
r_angle_other_deg	0.481
r_chiral_restr	0.093
r_bond_refined_d	0.009
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	2538
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	141

Software

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