5YLB | pdb_00005ylb

Crystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	18% MPEG 5000, 0.1M HEPES,pH7.0

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.506	α = 90
b = 80.386	β = 90
c = 81.996	γ = 90

Symmetry
Space Group	I 2 2 2

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 315r		2013-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97907	SSRF	BL17U1

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	1.79	57.4	99.9	0.079	2.69	8.7		20695

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3THP	1.79	57.4	20695	1123	98.46	0.1876	0.1853	0.2329	0.2527	RANDOM	33.226

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]
2.31			-3.6		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.346
r_dihedral_angle_4_deg	19.007
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	8.987
r_angle_refined_deg	1.18
r_angle_other_deg	0.634
r_chiral_restr	0.091
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1510
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing