2P63 | pdb_00002p63

Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	300	50%MPD, 100 mM (NH4)H2PO4 ph 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.816	α = 90
b = 37.816	β = 90
c = 298.118	γ = 120

Symmetry
Space Group	P 61

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	SBC	Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2005-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9788	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.67	49.69	99.3	0.0702	0.0349	21.15	9.81	6882	6756	8.4	8.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.73	98		0.1712	0.1228	8.47	6.95	383

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.67	49.69	8.47	8.47	6284	6284	472	99.08	0.22396	0.22396	0.21974	0.1959	0.27851	RANDOM	25.025

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]
3.17	1.59		3.17		-4.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.38
r_dihedral_angle_4_deg	23.917
r_dihedral_angle_3_deg	22.595
r_dihedral_angle_1_deg	5.045
r_scangle_it	2.044
r_mcangle_it	1.32
r_angle_refined_deg	1.27
r_scbond_it	1.264
r_mcbond_it	0.775
r_nbtor_refined	0.303
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.093
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1678
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
EPICS-based	data collection
data	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing