Experiment: 2OIC

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
2.99	58.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.894	α = 90
b = 141.321	β = 122.27
c = 88.263	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 210		2005-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

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	2.4	50	99.6	7.1	16	3.7		62496	3		58.1

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)
	2.4	2.49	96.7		0.511	2.1	2.9	6058

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	THROUGHOUT	PDB ENTRY 2OIB	2.4	48.17	59030	3147	99.86	0.22567	0.22285	0.2781	RANDOM	64.797

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]
3.21		1.11	-0.87		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.937
r_dihedral_angle_4_deg	22.439
r_dihedral_angle_3_deg	16.899
r_dihedral_angle_1_deg	5.516
r_scangle_it	2.304
r_angle_refined_deg	1.762
r_scbond_it	1.347
r_mcangle_it	1.302
r_mcbond_it	0.732
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.937
r_dihedral_angle_4_deg	22.439
r_dihedral_angle_3_deg	16.899
r_dihedral_angle_1_deg	5.516
r_scangle_it	2.304
r_angle_refined_deg	1.762
r_scbond_it	1.347
r_mcangle_it	1.302
r_mcbond_it	0.732
r_nbtor_refined	0.298
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.141
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8893
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	140

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 R01GM157729.