9HRB | pdb_00009hrb

A canonical homodimer of type III polyketide synthase from Aspergillus thesauricus IBT 34227

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E1H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M Tris (pH 8.5), 0.03 M MgCl 2 , 0.03 M CaCl 2 , 10% (w/v) PEG8000, and 20% (w/v) PEG200

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.39	α = 90
b = 89.97	β = 90
c = 141.243	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	100	PIXEL	DECTRIS EIGER X 16M		2024-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033210	PETRA III, DESY	P11

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	1.9	47.08	99.9	0.999	13.8	6.8		72348

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	1.9	1.94	100		0.772

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	45.026	72274	3657	99.827	0.171	0.1696	0.1721	0.2053	0.2075	37.384

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]
2.259			1.112		-3.372

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.378
r_dihedral_angle_3_deg	13.17
r_lrange_other	7.552
r_lrange_it	7.549
r_dihedral_angle_2_deg	7.384
r_dihedral_angle_1_deg	6.639
r_scangle_it	6.555
r_scangle_other	6.554
r_scbond_it	4.358
r_scbond_other	4.358
r_mcangle_it	3.87
r_mcangle_other	3.869
r_mcbond_it	2.85
r_mcbond_other	2.844
r_angle_refined_deg	1.755
r_angle_other_deg	0.571
r_symmetry_nbd_refined	0.314
r_nbd_refined	0.215
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.172
r_nbd_other	0.139
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5831
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing