1TFF | pdb_00001tff

Structure of Otubain-2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	288.15	14% PEG 4000, 0.1 M HEPES, pH 7.0, 12 % isopropanol and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 288.15K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.433	α = 90
b = 65.401	β = 90
c = 76.259	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	105	CCD	MARRESEARCH			M	MAD
2	1	x-ray	105	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97630, 0.97990, 0.98010	ESRF	BM30A
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97950	ESRF	ID14-4

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	2.1	100	99.7	0.085	18.11	27	14128	14128

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)
	2.1	2.18	100		0.273	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	49.39	13320	700	99.51	0.19125	0.19125	0.18792	0.25689	RANDOM	26.717

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]
-0.08			-0.82		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.707
r_scangle_it	6.521
r_scbond_it	4.341
r_mcangle_it	3.076
r_angle_refined_deg	2.382
r_mcbond_it	1.792
r_angle_other_deg	1.06
r_symmetry_vdw_other	0.319
r_nbd_other	0.253
r_nbd_refined	0.233
r_symmetry_hbond_refined	0.218
r_xyhbond_nbd_refined	0.187
r_symmetry_vdw_refined	0.18
r_chiral_restr	0.15
r_nbtor_other	0.096
r_bond_refined_d	0.028
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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	1826
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing