5NMC | pdb_00005nmc

Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EHV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2 and 20% v/v TFE

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.79	α = 90
b = 50.32	β = 90
c = 93.95	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2011-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.265	ELETTRA	5.2R

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	27.02	99.8	0.243	4.4	5.2		23500	3	-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	1.7	1.73	99.8		0.693	1.6	4.3

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	3EHV	1.7	27.02	22311	1136	99.66	0.22728	0.22477	0.24	0.27639	0.28	RANDOM	19.027

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]
-2.03			1.72		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.676
r_dihedral_angle_4_deg	23.772
r_dihedral_angle_3_deg	16.722
r_dihedral_angle_1_deg	6.926
r_long_range_B_refined	5.81
r_long_range_B_other	5.666
r_scangle_other	3.54
r_mcangle_it	2.516
r_mcangle_other	2.515
r_scbond_it	2.283
r_scbond_other	2.282
r_angle_refined_deg	2.087
r_mcbond_it	1.663
r_mcbond_other	1.63
r_angle_other_deg	1.144
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1750
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing