9PYJ | pdb_00009pyj

Crystal Structure of ZETA_2-Apo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		de novo designed model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M MgCl2, 0.1M Tris pH 8.5, 30% PEG4000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.21	α = 90
b = 94.865	β = 90
c = 50.375	γ = 90

Symmetry
Space Group	P 1 21 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 16M		2025-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97920	APS	24-ID-E

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	3.49	94.86	99	0.335	0.405	0.155	0.963	3.2	6.7		5069

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.49	3.82			0.934	0.442	0.613	1.8	6.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.49	50.426	5055	192	98.866	0.228	0.2254	0.2296	0.2829	0.2903	RANDOM	85.782

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]
-6.691		0.432	-1.36		8.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.124
r_dihedral_angle_6_deg	12.505
r_dihedral_angle_1_deg	5.563
r_dihedral_angle_2_deg	5.321
r_angle_refined_deg	1.111
r_angle_other_deg	0.427
r_nbd_refined	0.259
r_symmetry_xyhbond_nbd_refined	0.244
r_nbd_other	0.23
r_symmetry_nbd_other	0.211
r_symmetry_nbd_refined	0.201
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_other	0.117
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.007
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3953
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction