9N43 | pdb_00009n43

Crystal structure of none-heme iron enzyme (TqaM) from Trichoderma atroviride bound with iron

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	4.5	291	0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 4.5, 8% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.513	α = 90
b = 124.972	β = 90
c = 187.295	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 R 4M		2024-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	18.25	98.4	0.234	0.908	5.3	5.3		40872

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	2.6	2.71			0.568	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	18.25	1.4	40855	2045	98.48	0.262	0.2604	0.261	0.2917	0.2917	18.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.3678
f_angle_d	0.4865
f_chiral_restr	0.0421
f_plane_restr	0.0041
f_bond_d	0.0021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8706
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing