8KGA

SlNDPS1-AtcPT4 Chimera

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VPC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	Sodium malonate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.11	α = 90
b = 90.107	β = 90
c = 126.479	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER X 9M		2022-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.18	50	99.9	0.131	0.998	9.74	7		465239

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.31	99.5		3.06	0.576	0.72	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.182	48.883	35271	1783	99.878	0.206	0.2033	0.25	69.667

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]
3.049			1.911		-4.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.502
r_dihedral_angle_6_deg	17.502
r_lrange_it	11.884
r_lrange_other	11.883
r_scangle_it	9.496
r_scangle_other	9.495
r_mcangle_it	7.535
r_mcangle_other	7.533
r_scbond_it	6.427
r_scbond_other	6.425
r_dihedral_angle_1_deg	5.927
r_mcbond_other	5.261
r_mcbond_it	5.26
r_dihedral_angle_2_deg	2.427
r_angle_refined_deg	1.275
r_angle_other_deg	0.421
r_nbd_other	0.26
r_nbd_refined	0.218
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.154
r_ncsr_local_group_1	0.154
r_symmetry_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3767
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	40

Software

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