9S8A | pdb_00009s8a

Amuc0451_S1_20

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		298	20 % w/v PEG 3350, 0.1 M Bis-Tris propane 7.5, 0.02 M Sodium/potassium phosphate 40 mg/ml Amuc0451

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.66	α = 90
b = 59.9	β = 115.75
c = 123.72	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 EIGER2 S 16M		2022-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0	Diamond	I03

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	1.6	59.9	100	0.998	10.3	6.5		1291159

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	1.6	1.63			0.549	1.4

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	1.6	51.754	197782	9908	99.961	0.157	0.1556	0.1678	0.1915	0.1702	23.68

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]
2.642		0.096	-4.146		0.964

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.656
r_lrange_it	13.078
r_lrange_other	12.349
r_dihedral_angle_3_deg	12.106
r_scangle_it	8.552
r_scangle_other	8.539
r_dihedral_angle_2_deg	7.658
r_rigid_bond_restr	7.257
r_mcangle_other	6.979
r_mcangle_it	6.978
r_dihedral_angle_1_deg	6.893
r_scbond_it	6.002
r_scbond_other	5.986
r_mcbond_it	4.971
r_mcbond_other	4.971
r_angle_refined_deg	1.681
r_angle_other_deg	0.6
r_metal_ion_refined	0.28
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.176
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10611
Nucleic Acid Atoms
Solvent Atoms	948
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing