3ICU | pdb_00003icu

Protease-associated domain of the E3 ligase grail

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EK8	PDB ENTRY 2EK8, 1XF1
experimental model	PDB	1XF1	PDB ENTRY 2EK8, 1XF1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290.9	20% PEG 3350, 0.2 M NaH2PO4. PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.9K

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.795	α = 90
b = 65.795	β = 90
c = 136.524	γ = 90

Symmetry
Space Group	P 43 21 2

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		2009-06-25	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	2.1	25	100	0.101	30.7647	11.6	18428	18428		-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	2.1	2.18	99.9		0.748	3.633	10.2	1804

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 2EK8, 1XF1	2.1	25	17299	927	99.99	0.19576	0.19461	0.1927	0.2183	0.217	RANDOM	32.997

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]
0.75			0.75		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.432
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	12.762
r_dihedral_angle_1_deg	6.195
r_scangle_it	3.365
r_scbond_it	2.084
r_angle_refined_deg	1.768
r_mcangle_it	1.287
r_mcbond_it	0.701
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1286
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	14

Software

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