7P75

Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael addition reactions in substrate-free state

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	Protein was concentrated to 16 mg/ml in 10 mM potassium phosphate. Crystals grew from hanging-drop vapour diffusion experiments using 13% PEG 3350, 10% isopropanol and 0.1 M HEPES pH 7.5 as reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.634	α = 90
b = 67.497	β = 101.045
c = 73.657	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	CCD	ADSC QUANTUM 315		2021-06-06	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	1.229	47	96.9	0.057	0.081	0.057	0.99	6.9	2.3		128757

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	1.23	1.25			0.629	0.882	0.617	0.539		2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1P1X	1.23	47	128704	6430	96.803	0.149	0.1477	0.1714	17.444

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]
0.342		1.091	-1.004		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.728
r_dihedral_angle_3_deg	11.039
r_dihedral_angle_4_deg	10.763
r_dihedral_angle_1_deg	6.88
r_lrange_it	2.972
r_lrange_other	2.502
r_scangle_it	1.952
r_scangle_other	1.952
r_mcangle_other	1.734
r_mcangle_it	1.733
r_scbond_it	1.624
r_scbond_other	1.624
r_angle_other_deg	1.486
r_angle_refined_deg	1.371
r_mcbond_it	1.274
r_mcbond_other	1.269
r_rigid_bond_restr	1.014
r_symmetry_nbd_refined	0.28
r_nbd_other	0.221
r_nbd_refined	0.213
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.123
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.075
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3761
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement