Experiment: 3EO9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B2W	PDB ENTRY 1B2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	15mM citric acid, 12% w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.198	α = 90
b = 87.198	β = 90
c = 117.223	γ = 120

Symmetry
Space Group	P 31 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	IMAGE PLATE	RIGAKU RAXIS IV++	Confocal	2007-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	20	98.1	0.083	0.083	6.3	7.2	48198	47282	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	99.8		0.373	0.373	1.9	6.6	4699

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1B2W	1.8	20	1	1	45884	44966	2347	98	0.1907	0.1907	0.18932	0.2	0.21702	0.21	RANDOM	21.482

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]
-0.29	-0.15		-0.29		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.295
r_rigid_bond_restr	2.558
r_scangle_it	2.48
r_scbond_it	2.378
r_sphericity_free	2.141
r_angle_refined_deg	1.297
r_mcangle_it	1.151
r_sphericity_bonded	1.13
r_mcbond_it	0.664
r_nbd_refined	0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.295
r_rigid_bond_restr	2.558
r_scangle_it	2.48
r_scbond_it	2.378
r_sphericity_free	2.141
r_angle_refined_deg	1.297
r_mcangle_it	1.151
r_sphericity_bonded	1.13
r_mcbond_it	0.664
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.156
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3274
Nucleic Acid Atoms
Solvent Atoms	625
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
CNS	refinement
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

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.