9RQP | pdb_00009rqp

Human SMUG1 in complex with 5-fluorouracil

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 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
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.558	α = 90
b = 59.975	β = 90
c = 91.293	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 X 16M		2023-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.899	50.126	99.2	0.993	7.5	12.4		21518

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	1.899	1.932			0.708

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	1.899	50.126	21468	1104	98.899	0.193	0.1905	0.1905	0.2333	0.233	28.738

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]
-0.196			0.74		-0.544

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.053
r_dihedral_angle_3_deg	11.673
r_dihedral_angle_2_deg	10.03
r_lrange_other	6.46
r_lrange_it	6.435
r_dihedral_angle_1_deg	6.172
r_scangle_it	5.011
r_scangle_other	5.01
r_scbond_it	3.249
r_scbond_other	3.248
r_mcangle_it	2.979
r_mcangle_other	2.978
r_mcbond_it	2.082
r_mcbond_other	2.067
r_angle_refined_deg	1.63
r_angle_other_deg	0.52
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.182
r_nbd_other	0.166
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
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	103
Heterogen Atoms	37

Software

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