3MTN | pdb_00003mtn

Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I3T	PDB ENTRY 3I3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	291	11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
3.16	60.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.065	α = 90
b = 58.235	β = 121.19
c = 133.596	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	RIGAKU RAXIS IV		2010-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.7	20	99.7	0.112	12.64	3.5	31000	31000		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	95.4		0.659	2.08	3.1

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3I3T	2.7	19.61	29294	1553	99.91	0.22042	0.2177	0.27291	0.2566	RANDOM	53.866

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]
-0.05		-0.02	0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.071
r_dihedral_angle_4_deg	21.138
r_dihedral_angle_3_deg	19.968
r_dihedral_angle_1_deg	5.97
r_scangle_it	1.735
r_angle_refined_deg	1.197
r_scbond_it	1.021
r_mcangle_it	0.724
r_mcbond_it	0.376
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6255
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	18

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling