1YJ1

X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	CdCl2, PEG MME 2000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.872	α = 90
b = 50.395	β = 90
c = 92.941	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	CCD	ADSC QUANTUM 210		2004-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97926	APS	17-ID

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	1.3	20				51444	41081

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	1.3	1.4	35

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1UBQ	1.3	20	38985	2096	79.86	0.19637	0.19522	0.21769	RANDOM	7.427

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]
-0.53			0.39		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.324
r_dihedral_angle_4_deg	20.741
r_dihedral_angle_3_deg	14.551
r_dihedral_angle_1_deg	6.497
r_scangle_it	4.047
r_scbond_it	3.235
r_mcangle_it	1.902
r_angle_other_deg	1.806
r_angle_refined_deg	1.706
r_mcbond_it	1.652
r_mcbond_other	0.374
r_symmetry_vdw_refined	0.301
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.267
r_xyhbond_nbd_refined	0.261
r_symmetry_vdw_other	0.241
r_nbd_other	0.188
r_chiral_restr	0.17
r_metal_ion_refined	0.138
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1745
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	20

Software

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