Experiment: 8U0Z

CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN OF Coffea arabica UMP SYNTHASE

X-RAY DIFFRACTION

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, HANGING DROP	7.5	291	0.1 M Hepes pH 7.5 and 20% (w/v) PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.007	α = 90
b = 95.699	β = 90
c = 112.205	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 PILATUS3 X 6M		2023-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.399	48.4	97.3	0.056	0.99	20.4	11.4		103974			18.03

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.399	1.47	83.7		0.45	0.89	3	4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.399	47.849	1.35	103831	5129	97.16	0.1591	0.1581	0.1613	0.178	0.1808

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.931
f_angle_d	1.402
f_chiral_restr	0.105
f_bond_d	0.016
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3900
Nucleic Acid Atoms
Solvent Atoms	606
Heterogen Atoms	58

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing