4A3P | pdb_00004a3p

Structure of USP15 DUSP-UBL deletion mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PV1	PDB ENTRY 3PV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		1.9 M (NH4)2SO4, 100 MM HEPES PH 7.0, 200 MM KI.

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.95	α = 90
b = 44.25	β = 104.33
c = 56.15	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	CCD	ADSC QUANTUM 4r	DUAL SLITS		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	1.4	34.33	92.8	0.03	13.4	2.2		39193		13.4	27.2

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	1.4	1.47	95		0.2	3.9	2.2

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	PDB ENTRY 3PV1	1.4	27.2	37168	1981	92.27	0.15652	0.153	0.17	0.22126	0.23	RANDOM	18.149

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]
0.03		-0.13	0.04		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.109
r_sphericity_free	28.951
r_rigid_bond_restr	16.083
r_mcangle_it	15.308
r_dihedral_angle_4_deg	14.948
r_sphericity_bonded	13.999
r_mcbond_other	13.868
r_mcbond_it	13.509
r_dihedral_angle_3_deg	13.376
r_dihedral_angle_1_deg	5.667
r_angle_refined_deg	1.891
r_angle_other_deg	1.212
r_symmetry_vdw_other	0.505
r_symmetry_vdw_refined	0.441
r_symmetry_hbond_refined	0.324
r_nbd_refined	0.321
r_xyhbond_nbd_refined	0.264
r_nbd_other	0.236
r_nbtor_refined	0.191
r_chiral_restr	0.124
r_nbtor_other	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_xyhbond_nbd_other
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_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1713
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	5

Software

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