1UMH | pdb_00001umh

Structural basis of sugar-recognizing ubiquitin ligase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Tris, PEG400, Nickel Chloride, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.44	α = 90
b = 62.44	β = 90
c = 117.3	γ = 120

Symmetry
Space Group	P 32 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	293	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2002-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	100	99.9			18483	18483

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)
	2	2.11	99.9		0.278		10.1	2647

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-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	2	54.23	17470	945	99.64	0.15523	0.15523	0.15327	0.19229	RANDOM	29.192

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]
-0.36	-0.18		-0.36		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.651
r_dihedral_angle_1_deg	5.955
r_scbond_it	4.061
r_mcangle_it	2.585
r_angle_refined_deg	1.785
r_mcbond_it	1.354
r_angle_other_deg	0.964
r_symmetry_hbond_refined	0.334
r_symmetry_vdw_other	0.297
r_nbd_other	0.274
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.178
r_metal_ion_refined	0.158
r_chiral_restr	0.127
r_symmetry_vdw_refined	0.09
r_nbtor_other	0.089
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1489
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MLPHARE	phasing