8YQ3 | pdb_00008yq3

Structure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus

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, HANGING DROP	8.25	291	0.1 M Tris (base)-Bicine pH 8.25; 20% (v/v) PEG 500*MME; 10% (w/v) PEG 20000; 0.2 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D- Glucosamine)

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.184	α = 90
b = 53.052	β = 96.975
c = 101.643	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 EIGER2 S 9M		2023-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.52	100.891	99.6	0.1771	0.968	6.29	6.2		18944

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	2.52	2.61	99.79		1.202	0.29

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AlphaFold2	2.52	100.891	18913	912	99.889	0.223	0.2177	0.2265	0.3216	0.3279	RANDOM	49.958

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]
1.155		-2.009	-0.693		0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.229
r_dihedral_angle_6_deg	14.083
r_lrange_it	12.688
r_lrange_other	12.632
r_dihedral_angle_1_deg	7.389
r_dihedral_angle_2_deg	6.576
r_scangle_it	6.507
r_scangle_other	6.506
r_mcangle_it	6.18
r_mcangle_other	6.179
r_scbond_it	4.059
r_scbond_other	4.058
r_mcbond_it	3.952
r_mcbond_other	3.951
r_angle_refined_deg	1.486
r_angle_other_deg	0.504
r_nbd_refined	0.231
r_symmetry_nbd_other	0.211
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.182
r_nbd_other	0.175
r_symmetry_nbd_refined	0.161
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4049
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	97

Software

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