9GM2 | pdb_00009gm2

Human SMUG1 in complex with DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GGS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M diammonium hydrogen citrate pH 4.9, 60% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.072	α = 90
b = 84.366	β = 113.403
c = 88.259	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 PILATUS3 6M		2023-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6702	Diamond	I24

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	2.1	72.045	100	0.994	5.9	12.7		56982

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	2.1	2.16			0.328

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	2.1	72.045	47057	2374	79.681	0.209	0.2066	0.2058	0.2534	0.253	39.311

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]
-0.331		0.166	0.021		0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.575
r_dihedral_angle_3_deg	13.748
r_dihedral_angle_2_deg	7.696
r_dihedral_angle_1_deg	7.169
r_lrange_it	7.161
r_lrange_other	7.157
r_scangle_it	3.93
r_scangle_other	3.93
r_mcangle_it	2.526
r_mcangle_other	2.526
r_scbond_it	2.451
r_scbond_other	2.451
r_mcbond_it	1.454
r_mcbond_other	1.453
r_angle_refined_deg	1.425
r_angle_other_deg	0.426
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_other	0.226
r_symmetry_nbd_other	0.217
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_other	0.121
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.065
r_gen_planes_other	0.006
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d
r_dihedral_angle_other_2_deg

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7732
Nucleic Acid Atoms	970
Solvent Atoms	242
Heterogen Atoms

Software

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