1ZUO | pdb_00001zuo

Structure of Human Ubiquitin-Conjugating Enzyme (UBCi) Involved in Embryo Attachment and Implantation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.8	298	NACL, SODIUM CACODYLATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 5.8

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.442	α = 90
b = 126.442	β = 90
c = 104.872	γ = 90

Symmetry
Space Group	I 4 2 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	CCD	ADSC QUANTUM 210	MIRRORS	2005-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1		CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	27.07	91.4	0.059	22.5	2.8		36041		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	94.2		2.4	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.8	27.08	36041	34253	1788	91.43	0.20143	0.1998	0.1999	0.23239	0.2343	RANDOM	30.471

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]
1.28			1.28		-2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.412
r_dihedral_angle_4_deg	18.012
r_dihedral_angle_3_deg	13.879
r_scangle_it	5.992
r_dihedral_angle_1_deg	5.815
r_scbond_it	4.159
r_mcangle_it	3.249
r_mcbond_it	2.259
r_angle_refined_deg	1.476
r_symmetry_vdw_refined	0.392
r_nbtor_refined	0.31
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2402
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	8

Software

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