6TUV | pdb_00006tuv

Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JKN	5JKN, 1UBQ
experimental model	PDB	1UBQ	5JKN, 1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.862	α = 90
b = 73.862	β = 90
c = 202.867	γ = 90

Symmetry
Space Group	P 41 2 2

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 6M		2015-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.939274	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.16	41.81	99.9	0.087	0.094	0.036	0.999	13.9	6.8		31102

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.23	99.9		0.955	1.028	0.378	0.889	4.1	7.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5JKN, 1UBQ	2.16	41.37	29517	1517	99.79	0.2096	0.2075	0.2224	0.249	0.2601	RANDOM	49.244

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]
2.18			2.18		-4.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.473
r_dihedral_angle_3_deg	17.096
r_dihedral_angle_4_deg	16.779
r_dihedral_angle_1_deg	7.319
r_angle_refined_deg	1.608
r_angle_other_deg	1.263
r_chiral_restr	0.065
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	3451
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction