9FD8 | pdb_00009fd8

Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-chloro-cinnamaldehyde

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Crystal structure of the apo enzyme was used as starting model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	Protein was concentrated to 8 mg/mL in 20 mM potassium phosphate, pH 7. Crystallization conditions: 0-4% 2-propanol, 22-24% PEG 3350 in 0.1 M HEPES, pH 7.5. The Schiff-base complex was obtained by brief soaking (about 30 seconds) in saturated ligand solution prepared with crystallization solution plus 25% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.084	α = 90
b = 72.47	β = 96.2
c = 70.885	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 PILATUS3 6M		2022-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

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	1.58	48	98.7	0.084	0.101	0.055	0.996	7.2	3.2		65329

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	1.58	1.61		89.6	0.664	0.862	0.542	0.455		2.2

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	FOURIER SYNTHESIS	THROUGHOUT	1.58	47.85	62201	3107	98.56	0.16514	0.16419	0.178	0.18472	0.1975	RANDOM	18.965

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]
-0.92		0.16	0.84		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.543
r_dihedral_angle_2_deg	8.214
r_dihedral_angle_1_deg	6.271
r_long_range_B_refined	5.574
r_long_range_B_other	5.475
r_scangle_other	4.488
r_scbond_it	2.854
r_scbond_other	2.854
r_mcangle_it	1.95
r_mcangle_other	1.95
r_angle_refined_deg	1.601
r_mcbond_it	1.307
r_mcbond_other	1.299
r_angle_other_deg	0.545
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	3658
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	26

Software

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