4FH1 | pdb_00004fh1

S. cerevisiae Ubc13-N79A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JBB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10.3	296	0.1 M CHES, pH 10.3, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.026	α = 90
b = 77.026	β = 90
c = 68.35	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	110	IMAGE PLATE	MAR scanner 345 mm plate		2012-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033	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	2.65	66.71	99.8	0.139	12.3	4.9		7065	2	1

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	2.65	2.7	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1JBB	2.61	33.35	7410	7065	345	99.36	0.2199	0.21866	0.22	0.24553	0.24	RANDOM	56.209

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]
1.43	0.72		1.43		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.312
r_dihedral_angle_4_deg	19.158
r_dihedral_angle_3_deg	18.075
r_dihedral_angle_1_deg	5.141
r_angle_refined_deg	1.045
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1109
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling