9GLF | pdb_00009glf

Anthraquinone Pigment Production Regulated by Cinnamic Acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HXA	AntI from P. luminescens catalyses terminal polyketide shortening in the biosynthesis of anthraquinones

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	293	0.1 M NaAc, 0.1M HEPES, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.38	α = 90
b = 154.46	β = 90
c = 91.06	γ = 90

Symmetry
Space Group	C 2 2 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	DECTRIS EIGER X 16M		2022-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	30	98.4	0.03	20.2	4.5		74543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.5	98.6		0.662	2	4.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	30	70809	3727	98.42	0.1488	0.1472	0.147	0.1809	0.1807	RANDOM	25.737

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]
-0.77			-0.06		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.244
r_dihedral_angle_4_deg	17.615
r_dihedral_angle_3_deg	12.418
r_dihedral_angle_1_deg	6.903
r_angle_other_deg	1.403
r_rigid_bond_restr	1.394
r_angle_refined_deg	1.365
r_chiral_restr	0.075
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3049
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing