3BI7 | pdb_00003bi7

Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well solution mixed in 1:1 ratio with a water solution containing 20% (w/v) Sucrose, 4% (w/v) Glucose, 18% (v/v) Glycerol and 18% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.975	α = 90
b = 65.975	β = 90
c = 96.061	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 300 mm CCD	Mirrors	2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97943	APS	23-ID-B

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	1.7	50	100	0.153	24.15	9.9	27377	27377		-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)
	1.7	1.76	100		0.9	2.1	6.2	2670

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.7	32.99	25677	1369	99.39	0.16043	0.15851	0.19658	0.1569	RANDOM	15.105

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]
0.77	0.38		0.77		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.958
r_dihedral_angle_4_deg	20.645
r_dihedral_angle_3_deg	13.326
r_dihedral_angle_1_deg	5.149
r_scangle_it	3.265
r_scbond_it	2.207
r_angle_refined_deg	1.519
r_mcangle_it	1.471
r_mcbond_it	1.055
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.261
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.121
r_symmetry_hbond_refined	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1547
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing