2J9W | pdb_00002j9w

Structural insight into the ESCRT-I-II link and its role in MVB trafficking

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SE DATASET FROM SEMET SUBSTITUTED CRYSTAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		15-25% PEG 600, 0.15M POTASSIUM THIOCYANATE, 0.2M SODIUM CHLORIDE, 0.1M GUANIDINE HYDROCHLORIDE, 0.1M SODIUM CACODYLATE PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.997	α = 90
b = 89.713	β = 95.13
c = 40.384	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 CCD	TORODIAL MIRROR	2006-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.2	44.86	88.3	0.1	10.57	4.3		8573

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	2.2	2.23	45.7		0.33	3.28	1.17

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	SE DATASET FROM SEMET SUBSTITUTED CRYSTAL	1.3	44.86	37809	2027	88.2	0.202	0.2	0.2	0.228	0.23	RANDOM	16.59

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]
0.62		-0.14	-0.35		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.52
r_dihedral_angle_4_deg	18.99
r_dihedral_angle_3_deg	14.919
r_dihedral_angle_1_deg	4.421
r_scangle_it	4.382
r_scbond_it	3.004
r_mcangle_it	1.773
r_angle_refined_deg	1.502
r_mcbond_it	1.162
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.268
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	1638
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms

Software

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