9S8X | pdb_00009s8x

Amuc0953_S1_20 in complex with D-Galactose

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 % PEG 3350 0.2 M Sodium Iodide 55 mg/ml Amuc0953 with 100 mM D-Galactose

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.28	α = 90
b = 187.28	β = 90
c = 221.77	γ = 90

Symmetry
Space Group	I 41

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 I04	1.0	Diamond	I04

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	2.9	78.476	100	0.998	9.9	6.5		1156298

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	2.9	2.95			0.641

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	2.9	78.476	84299	4384	99.956	0.214	0.2118	0.2095	0.2566	0.2511	90.956

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]
-2.084			-2.084		4.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.136
r_dihedral_angle_6_deg	14.467
r_lrange_it	13.935
r_lrange_other	13.935
r_dihedral_angle_2_deg	10.994
r_scangle_it	10.223
r_scangle_other	10.222
r_mcangle_it	8.407
r_mcangle_other	8.407
r_dihedral_angle_1_deg	7.726
r_scbond_it	6.776
r_scbond_other	6.776
r_mcbond_it	5.666
r_mcbond_other	5.666
r_angle_refined_deg	1.558
r_angle_other_deg	0.538
r_metal_ion_refined	0.502
r_symmetry_xyhbond_nbd_refined	0.268
r_nbd_refined	0.234
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.18
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.072
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.006
r_gen_planes_refined	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	19044
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	30

Software

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