2OJR | pdb_00002ojr

Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	298	0.1M HEPES pH 7.5, 3.7 M NaCl, 33% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.87	α = 90
b = 57.87	β = 90
c = 115.26	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	100	CCD	ADSC QUANTUM 315	SI-111 MONO, MIRRORS	2005-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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	2.6	50	98.4	0.127	15.8	8.5		7214

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.6	2.69	87.7		0.378	2.8	4.4

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	2.6	30.49	6147	6147	285	100	0.218	0.216	0.21	0.254	0.26	RANDOM	48.73

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]
6	3		6		-8.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.403
r_dihedral_angle_3_deg	19.897
r_dihedral_angle_4_deg	10.225
r_dihedral_angle_1_deg	7.514
r_scangle_it	2.171
r_angle_other_deg	1.959
r_angle_refined_deg	1.608
r_scbond_it	1.389
r_mcangle_it	0.908
r_mcbond_it	0.766
r_symmetry_hbond_refined	0.32
r_nbd_refined	0.286
r_symmetry_vdw_refined	0.27
r_symmetry_vdw_other	0.267
r_xyhbond_nbd_refined	0.258
r_nbd_other	0.238
r_nbtor_refined	0.196
r_chiral_restr	0.18
r_metal_ion_refined	0.121
r_nbtor_other	0.11
r_mcbond_other	0.085
r_bond_refined_d	0.013
r_bond_other_d	0.008
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	871
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction