8JRD

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	30% PEG 4000, 0.2 M ammonium acetate, 0.1M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.61	α = 90
b = 97.47	β = 90
c = 157.54	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 9M		2020-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.00000	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.83	50	100	0.22	0.997	12.94	15.66		75109

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.94	100		1.33	0.745	2.29	12.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.83	48.78	71283	3744	99.99	0.15194	0.1502	0.18514	RANDOM	22.515

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]
-0.63			0.28		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.727
r_dihedral_angle_4_deg	17.665
r_dihedral_angle_3_deg	13.969
r_long_range_B_refined	6.974
r_long_range_B_other	6.838
r_dihedral_angle_1_deg	6.552
r_scangle_other	5.419
r_scbond_it	3.636
r_scbond_other	3.636
r_mcangle_other	2.332
r_mcangle_it	2.327
r_angle_refined_deg	1.717
r_mcbond_it	1.71
r_mcbond_other	1.694
r_angle_other_deg	1.417
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	5988
Nucleic Acid Atoms
Solvent Atoms	703
Heterogen Atoms	207

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing