9BCZ

Chicken 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1 (PLCZ1) in complex with calcium and phosphorylated threonine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q2VRL0-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.1 M NaHEPES, MOPs acidic pH 7.5, 20% PEG 550 MME & 10% PEG 20,000, 0.2 M Monosaccharides

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.182	α = 90
b = 85.539	β = 112.04
c = 98.433	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	265735	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2024-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95307	CLSI	08ID-1

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	1.99	50	94.7	0.163	0.178	0.07	0.989	6.4	6		60478

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	2.03	75.8		0.927	1.031	0.443	0.663		4.3

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	1.99	49.59	57477	2998	94.07	0.17439	0.17287	0.20412	RANDOM	28.353

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]
-0.34		-1.91	-1.77		2.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.475
r_dihedral_angle_2_deg	8.501
r_long_range_B_refined	7.67
r_long_range_B_other	7.651
r_dihedral_angle_1_deg	7.099
r_scangle_other	6
r_mcangle_it	4.078
r_mcangle_other	4.078
r_scbond_it	3.875
r_scbond_other	3.859
r_mcbond_it	2.748
r_mcbond_other	2.736
r_angle_refined_deg	1.581
r_angle_other_deg	0.507
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	4818
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing