8S7Z

Urethanase umg-sp1 without inhibitor or substrate displays flexible active site loops

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	8.5	293	30% (v/v) isopropanol, 0.2 M ammonium acetate, 0.1 M Tris pH 8.5 Cryo: 10% glycerol added

Crystal Properties
Matthews coefficient	Solvent content
2.06	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.175	α = 89.994
b = 76.792	β = 112.646
c = 95.068	γ = 113.64

Symmetry
Space Group	P 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 EIGER X 16M		2023-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.67	45	97.5	0.35	0.99	6.1	8.9		44551		-3	65

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.85	97.5		2.18	0.53	1.3	9.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.67	44.538	44199	2194	97.062	0.263	0.2603	0.3227	random selection	56.551

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]
3.331	1.459	1.298	-0.957	0.271	-3.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.853
r_dihedral_angle_6_deg	14.558
r_lrange_it	11.977
r_lrange_other	11.977
r_dihedral_angle_2_deg	10.834
r_mcangle_other	8.638
r_mcangle_it	8.637
r_scangle_it	8.468
r_scangle_other	8.467
r_dihedral_angle_1_deg	7.753
r_mcbond_it	5.649
r_mcbond_other	5.645
r_scbond_it	5.396
r_scbond_other	5.393
r_angle_refined_deg	1.865
r_angle_other_deg	0.632
r_symmetry_nbd_refined	0.353
r_symmetry_xyhbond_nbd_refined	0.256
r_nbd_other	0.252
r_nbd_refined	0.234
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.085
r_ncsr_local_group_2	0.075
r_ncsr_local_group_1	0.072
r_ncsr_local_group_5	0.065
r_ncsr_local_group_6	0.065
r_ncsr_local_group_3	0.062
r_ncsr_local_group_4	0.05
r_bond_refined_d	0.009
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	10821
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

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