Experiment: 8QMT

Succinic semialdehyde dehydrogenase from E. coli with Q262R substitution and bound NAD+, succinic semialdehyde

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	14.8 mg/mL of SAD_Q262R in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was complemented with 5 mM NAD+. The enzyme was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, pH 7.5 , 20 % (w/v) PEG4000. The final drop size was 3 uL. The drop was complemented with 6 mM succininc semialdehyde and 25 % (v/v) PEG400 before flash freezing the crystals in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.71	α = 90
b = 115.11	β = 90
c = 179.38	γ = 90

Symmetry
Space Group	P 21 21 21

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		2023-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.8	29.55	98.6	0.098	0.102	0.9990000000000001	16.73	13.8		174478

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			1.6	1.663	0.8420000000000001

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	29.55	1.34	174080	1999	98.45	0.1805	0.1802	0.1798	0.2054	0.2047

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.136
f_angle_d	0.871
f_chiral_restr	0.053
f_plane_restr	0.013
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13912
Nucleic Acid Atoms
Solvent Atoms	1294
Heterogen Atoms	204

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing