9XZP | pdb_00009xzp

Crystal structure of AI-designed homodimer MIYEI

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	8.5	277	Morpheus G9: 30.0% w/v 550M_20K; 0.1 M MB3 pH 8.5; 0.1 M MCA

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.093	α = 90
b = 53.473	β = 112.443
c = 55.786	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 EIGER2 X CdTe 16M		2025-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	1.773	36.155	99.9	0.0987	0.1066	0.0399	0.997	9.46	6.92		14102

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)
	1.773	1.803	99.6		1.1616	1.2633	0.4907	0.688	1.43	6.48	713

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	1.773	36.155	14102	700	99.915	0.192	0.1894	0.1975	0.245	0.2567	37.01

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]
-1.157		1.944	-1.832		1.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.356
r_dihedral_angle_3_deg	11.372
r_lrange_it	6.542
r_lrange_other	6.49
r_dihedral_angle_1_deg	6.194
r_scangle_it	4.906
r_scangle_other	4.903
r_mcangle_it	3.832
r_mcangle_other	3.832
r_scbond_it	3.197
r_scbond_other	3.194
r_mcbond_it	2.572
r_mcbond_other	2.568
r_angle_refined_deg	1.355
r_dihedral_angle_2_deg	0.565
r_angle_other_deg	0.496
r_nbd_refined	0.201
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.151
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.118
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_symmetry_nbd_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1120
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms

Software

Software
Software Name	Purpose
autoPROC	data processing
Aimless	data scaling
TRUNCATE	data processing
REFMAC	refinement
XDS	data reduction
PHASER	phasing