9FD9 | pdb_00009fd9

Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-nitro-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 initial 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
2.13	42.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.095	α = 90
b = 72.531	β = 96.27
c = 70.688	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 PILATUS 6M		2022-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	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	1.52	47.81	95.5	0.09	0.115	0.072	0.988	7	2.3		70796

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	1.52	1.55		93.6	1.155	1.471	0.9	0.312		2.4

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	1.52	41.73	67356	3406	95.28	0.18777	0.18633	0.1993	0.21755	0.2308	RANDOM	20.473

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]
-0.35		0.04	0.69		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.214
r_dihedral_angle_2_deg	9.532
r_dihedral_angle_1_deg	6.542
r_long_range_B_refined	5.27
r_long_range_B_other	5.212
r_scangle_other	4.068
r_scbond_it	2.605
r_scbond_other	2.605
r_mcangle_it	1.991
r_mcangle_other	1.991
r_angle_refined_deg	1.782
r_mcbond_it	1.362
r_mcbond_other	1.331
r_angle_other_deg	0.597
r_chiral_restr	0.091
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
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	3642
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	30

Software

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