9LFT | pdb_00009lft

Biochemical and structural characterization of a novel 4-hydroxyphenylacetate-3-monooxygenase from Geobacillus mahadii Geo-05

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		293	0.8M Sodium formate, 0.1M Sodium cacodylate, 25% w/v PEG200 MME

Crystal Properties
Matthews coefficient	Solvent content
2.04	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.571	α = 90
b = 108.202	β = 99.46
c = 99.055	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2024-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953738	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.4	108.2	100	0.188	0.203	0.078	0.992	6.9	6.7		73743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.45	99.7		1.262	1.389	0.801	0.589	1.6	5.7

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	2.4	97.9	70078	3637	99.95	0.18714	0.18398	0.1893	0.24989	0.2488	RANDOM	37.125

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]
1.55		0.11	-1.03		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.986
r_dihedral_angle_2_deg	12.165
r_dihedral_angle_1_deg	6.907
r_long_range_B_refined	4.543
r_long_range_B_other	4.543
r_scangle_other	3.612
r_mcangle_it	2.528
r_mcangle_other	2.528
r_scbond_it	2.268
r_scbond_other	2.268
r_angle_refined_deg	1.704
r_mcbond_it	1.655
r_mcbond_other	1.655
r_angle_other_deg	0.587
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15417
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	76

Software

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