9U3O | pdb_00009u3o

Crystal structure of Chi430 mutant E176A in the substrate complex

X-RAY DIFFRACTION

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Serial Crystallography (SX)

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	4.5	290	0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.676	α = 90
b = 49.858	β = 125.616
c = 92.602	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 EIGER X 16M		2025-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.35	60.58	99.8	0.974	7.4	6		98938			6.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.39			0.189	2.5	4.4

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	1.35	49.506	98914	4902	99.769	0.185	0.1842	0.1936	0.2033	0.2112	10.787

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]
-0.057		0.244	-0.414		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.13
r_dihedral_angle_3_deg	12.533
r_dihedral_angle_1_deg	6.28
r_lrange_it	4.679
r_lrange_other	4.664
r_dihedral_angle_2_deg	4.058
r_scangle_it	3.814
r_scangle_other	3.814
r_scbond_other	2.438
r_scbond_it	2.436
r_mcangle_it	1.97
r_mcangle_other	1.969
r_angle_refined_deg	1.959
r_mcbond_it	1.269
r_mcbond_other	1.269
r_angle_other_deg	0.69
r_nbd_refined	0.241
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.16
r_nbd_other	0.149
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.056
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3238
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing