7BUR

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate (pH 5.6).

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.64	α = 90
b = 97.99	β = 90
c = 157.81	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		2019-07-11	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)	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	1.82	47.73	100	0.181	0.188	0.999	15.76	13.35		1023907

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	1.82	1.93	99.9		1.868	1.946	0.705	1.78	12.72

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	6DXA	1.82	47.73	76721	3904	99.927	0.153	0.1506	0.1926	27.319

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]
-1.821			0.561		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.283
r_dihedral_angle_4_deg	15.644
r_dihedral_angle_3_deg	13.881
r_lrange_it	7.786
r_lrange_other	7.705
r_dihedral_angle_1_deg	6.663
r_scangle_it	5.861
r_scangle_other	5.86
r_scbond_it	3.964
r_scbond_other	3.954
r_mcangle_other	2.696
r_mcangle_it	2.691
r_mcbond_it	1.988
r_mcbond_other	1.975
r_angle_refined_deg	1.633
r_angle_other_deg	1.39
r_nbd_refined	0.207
r_nbd_other	0.191
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5978
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	92

Software

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