4A20

Crystal structure of the Ubl domain of Mdy2 (Get5) at 1.78A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M62	PDB ENTRY 3M62

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5		3 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE PH 5.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN AT 6MG/ML, HANGING DROP VAPOUR DIFFUSION.

Crystal Properties
Matthews coefficient	Solvent content
2.83	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.19	α = 90
b = 47.19	β = 90
c = 78.41	γ = 120

Symmetry
Space Group	P 32 2 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	CCD	ADSC CCD		2011-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.78	40.87	99.8	0.06	5.75	7.72		10128

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.88	100		0.35	2.2	7.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3M62	1.78	19.77	9603	486	99.72	0.20327	0.20113	0.24825	RANDOM	24.108

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.851
r_dihedral_angle_3_deg	14.315
r_dihedral_angle_1_deg	5.925
r_scangle_it	5.358
r_scbond_it	3.576
r_mcangle_it	2.054
r_angle_refined_deg	1.987
r_mcbond_it	1.249
r_angle_other_deg	0.968
r_symmetry_hbond_refined	0.72
r_mcbond_other	0.383
r_nbd_refined	0.221
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.165
r_symmetry_vdw_other	0.155
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.114
r_nbtor_other	0.095
r_bond_refined_d	0.024
r_xyhbond_nbd_other	0.023
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	622
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing