Experiment: 2OID

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OIB	PDB ENTRY 2OIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2.3M sodium malonate, 0.1M sodium acetate, 0.01M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.116	α = 90
b = 138.973	β = 126.43
c = 89.198	γ = 90

Symmetry
Space Group	C 1 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	200	CCD	ADSC QUANTUM 315		2005-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.97943	SSRL	BL9-1

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	2.3	50	99.9	0.112	8.9			63527	3		50.8

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	DIFFERENCE FOURIER	THROUGHOUT	PDB ENTRY 2OIB	2.3	49.94	60299	3217	99.35	0.24381	0.24096	0.29542	RANDOM	53.347

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]
2.63		0.75	-2.31		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.911
r_dihedral_angle_4_deg	19.372
r_dihedral_angle_3_deg	17.344
r_dihedral_angle_1_deg	5.663
r_scangle_it	2.453
r_scbond_it	1.511
r_angle_refined_deg	1.366
r_mcangle_it	1.24
r_mcbond_it	0.711
r_symmetry_hbond_refined	0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.911
r_dihedral_angle_4_deg	19.372
r_dihedral_angle_3_deg	17.344
r_dihedral_angle_1_deg	5.663
r_scangle_it	2.453
r_scbond_it	1.511
r_angle_refined_deg	1.366
r_mcangle_it	1.24
r_mcbond_it	0.711
r_symmetry_hbond_refined	0.51
r_symmetry_vdw_refined	0.341
r_nbtor_refined	0.299
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8518
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.