9KAH | pdb_00009kah

Crystal Structure of Chalcone Syntase and Chalcone Isomerase-like Protein Complex from Physcomitrella patens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		CHS-CHIL complex model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3350, potassium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.9	α = 74.438
b = 88.87	β = 74.318
c = 117.97	γ = 68.803

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 9M		2023-10-19	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	1.92	50	98.9	0.17	0.986	5.16	2.89		216275

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	1.92	2.04	99.1		1.13	0.61	1.01	2.94

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.92	49.186	216275	10913	99.003	0.179	0.1773	0.1768	0.2126	0.2164	28.82

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]
-0.798	-0.806	-0.882	-0.904	1.529	1.166

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.848
r_dihedral_angle_3_deg	14.28
r_lrange_it	6.702
r_lrange_other	6.62
r_scangle_it	6.269
r_scangle_other	6.269
r_dihedral_angle_1_deg	5.936
r_scbond_it	4.945
r_scbond_other	4.945
r_mcangle_it	4.227
r_mcangle_other	4.226
r_dihedral_angle_2_deg	3.723
r_mcbond_it	3.634
r_mcbond_other	3.634
r_angle_refined_deg	1.538
r_angle_other_deg	0.709
r_symmetry_nbd_other	0.213
r_nbd_refined	0.208
r_nbd_other	0.182
r_chiral_restr	0.178
r_nbtor_refined	0.178
r_ncsr_local_group_12	0.131
r_ncsr_local_group_8	0.125
r_ncsr_local_group_10	0.125
r_ncsr_local_group_7	0.123
r_ncsr_local_group_6	0.117
r_ncsr_local_group_9	0.117
r_symmetry_nbd_refined	0.095
r_ncsr_local_group_11	0.094
r_ncsr_local_group_5	0.092
r_ncsr_local_group_3	0.091
r_ncsr_local_group_1	0.088
r_ncsr_local_group_2	0.088
r_ncsr_local_group_4	0.088
r_symmetry_nbtor_other	0.08
r_xyhbond_nbd_refined	0.077
r_symmetry_xyhbond_nbd_refined	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18156
Nucleic Acid Atoms
Solvent Atoms	2644
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing