8B35 | pdb_00008b35

Chalcone synthase from Hordeum vulgare complexed with CoA and naringenin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16% Glycerol; 8% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.908	α = 90
b = 95.981	β = 90
c = 138.338	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	291	PIXEL	DECTRIS EIGER X 16M		2022-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	2	48.037	99.9	0.087	0.094	0.036	0.999	19.8	13.2		67109

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	2	2.05			0.465	0.503	0.19	0.979		13.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8B32	2	48.037	67037	3335	99.869	0.161	0.1589	0.17	0.1934	0.2	29.158

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]
0.315			2.247		-2.562

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.744
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	13.995
r_lrange_it	7.175
r_lrange_other	7.152
r_scangle_it	6.271
r_scangle_other	6.27
r_dihedral_angle_1_deg	6.147
r_scbond_it	4.313
r_scbond_other	4.313
r_mcangle_it	3.326
r_mcangle_other	3.325
r_mcbond_it	2.546
r_mcbond_other	2.542
r_angle_refined_deg	1.658
r_angle_other_deg	1.445
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.187
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.139
r_chiral_restr	0.086
r_ncsr_local_group_1	0.082
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5804
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	136

Software

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