9GGS | pdb_00009ggs

Human SMUG1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OE4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1 M Buffer System 3 pH 8.4, 80 % (v/v) P500MME_P20K, 0.12 M Alcohols Mix (Morpheus Screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.045	α = 90
b = 60.585	β = 90
c = 91.964	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	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	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	1.38	50.6	98.2	0.999	16.1	12.2		56140

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	1.38	1.4			0.764

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	1.38	50.593	56070	2849	98.181	0.153	0.1516	0.1518	0.173	0.1733	17.622

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]
-0.267			0.65		-0.384

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.75
r_dihedral_angle_2_deg	12.47
r_dihedral_angle_3_deg	11.732
r_lrange_it	6.198
r_lrange_other	6.138
r_dihedral_angle_1_deg	5.918
r_scangle_it	4.992
r_scangle_other	4.99
r_scbond_it	3.395
r_scbond_other	3.394
r_mcangle_other	2.315
r_mcangle_it	2.301
r_angle_refined_deg	2.109
r_mcbond_it	1.51
r_mcbond_other	1.508
r_angle_other_deg	0.7
r_nbd_refined	0.235
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.184
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.136
r_chiral_restr	0.111
r_symmetry_xyhbond_nbd_other	0.1
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1927
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	25

Software

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