9ETO | pdb_00009eto

PsiK from Psilocybe cubensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	100 mM HEPES pH 7.5, 2 M ammonium sulfate, 2% PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.82	α = 90
b = 70.14	β = 95.837
c = 118.9	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 X 2M	KB mirror	2022-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	2.54	43.108	99.9	0.275	0.299	0.991	6.39	6.63		30400			60.6

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	2.54	2.61	99.9		2.641	2.859	0.35	0.91	6.85

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	2.54	43.108	30399	1483	99.859	0.2	0.1974	0.204	0.2433	0.2451	62.899

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]
1.121		1.009	-0.192		-1.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.071
r_dihedral_angle_6_deg	13.711
r_lrange_it	9.22
r_lrange_other	9.22
r_scangle_it	6.933
r_scangle_other	6.933
r_dihedral_angle_2_deg	6.913
r_dihedral_angle_1_deg	6.882
r_mcangle_it	5.536
r_mcangle_other	5.536
r_scbond_it	4.355
r_scbond_other	4.354
r_mcbond_it	3.496
r_mcbond_other	3.493
r_angle_refined_deg	1.689
r_angle_other_deg	0.551
r_nbd_refined	0.219
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.151
r_nbd_other	0.133
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.074
r_ncsr_local_group_1	0.063
r_symmetry_nbd_refined	0.052
r_symmetry_xyhbond_nbd_refined	0.031
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5684
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	101

Software

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