8WLW

Crystal structure of DelP123_Msd in complex with 5-azauracil

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XKO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1M Bis-Tris pH 6.4, 20% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.75	α = 90
b = 85.3	β = 102.491
c = 76.46	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2022-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	1.538	74.66	99.2	0.99	11.69	5.6		86243

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	1.538	1.578			0.84

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	1.538	74.65	86239	4298	99.218	0.178	0.1763	0.1909	0.2087	0.2215	17.242

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]
1.645		-0.775	-0.781		-0.474

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.568
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_2_deg	7.346
r_dihedral_angle_1_deg	5.584
r_lrange_it	4.986
r_lrange_other	4.959
r_scangle_it	4.293
r_scangle_other	4.292
r_scbond_it	2.801
r_scbond_other	2.801
r_mcangle_it	2.351
r_mcangle_other	2.351
r_mcbond_it	1.638
r_mcbond_other	1.619
r_angle_refined_deg	1.611
r_angle_other_deg	0.546
r_symmetry_nbd_refined	0.442
r_nbd_other	0.31
r_nbd_refined	0.237
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.115
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.025
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4719
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	60

Software

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