Experiment: 7MIC

Maize rayado fino virus protease in complex with Ubiquitin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MIA	7MIA, IUBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.8	277	100 mM phosphate citrate buffer (pH 3.8), 200 mM lithium sulfate and 25 % PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.72	α = 90
b = 75.72	β = 90
c = 79.56	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2019-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.541870

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	2.09	31.16	96.56	0.91	26.62	2		13343			16.94

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	2.09	2.17			0.85

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	7MIA, IUBQ	2.09	31.16	12892	1296	96.61	0.2107	0.2048	0.204	0.2628	0.2628	21.69

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	6.021
f_angle_d	0.5328
f_chiral_restr	0.0385
f_plane_restr	0.0036
f_bond_d	0.0021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1675
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	16

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing