9EQH | pdb_00009eqh

WWP2 WW2-2,3-linker-HECT (WWP2-LH)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TJ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	289	100 mM MMT pH 6.0, 25 % PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.009	α = 90
b = 90.27	β = 90
c = 111.177	γ = 90

Symmetry
Space Group	P 21 21 21

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		2023-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9795	Diamond	I24

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	2.046	70.079	99.5	0.19	0.205	0.075	0.994	6.9	6.7		28618			33.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.046	5.552	99.9		0.486

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	70.079	28369	1357	99.272	0.216	0.2134	0.22	0.2749	0.28	51.688

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]
-2.44			3.221		-0.781

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.128
r_dihedral_angle_6_deg	15.622
r_lrange_other	13.083
r_lrange_it	13.067
r_scangle_it	10.053
r_scangle_other	10.052
r_dihedral_angle_2_deg	9.95
r_mcangle_it	8.775
r_mcangle_other	8.773
r_dihedral_angle_1_deg	7.945
r_scbond_it	6.785
r_scbond_other	6.784
r_mcbond_it	6.399
r_mcbond_other	6.396
r_angle_refined_deg	2.222
r_angle_other_deg	1.011
r_nbd_refined	0.186
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.138
r_symmetry_nbd_other	0.137
r_chiral_restr	0.123
r_nbd_other	0.118
r_symmetry_nbd_refined	0.109
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_refined	0.057
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3518
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing