Experiment: 3EBO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HLF	PDB entry 1HLF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	286	BES, EDTA, pH 6.7, SMALL TUBES, temperature 286K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.834	α = 90
b = 128.834	β = 90
c = 116.635	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MAR CCD 165 mm		2008-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.038	MAX II	I911-2

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	1.9	91.29	97.3	0.055	15.6	5.3	75437	71586		-3	27.4

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)
1	1.9	1.93	96.7		0.488	4.4	5.4	5152

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1HLF	1.9	32.23	71586	3782	97.3	0.19573	0.19449	0.21957	RANDOM	31.01

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]
0.49			0.49		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.78
r_dihedral_angle_4_deg	18.182
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_1_deg	5.065
r_scangle_it	1.931
r_scbond_it	1.19
r_angle_refined_deg	1.012
r_mcangle_it	0.88
r_mcbond_it	0.523
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.78
r_dihedral_angle_4_deg	18.182
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_1_deg	5.065
r_scangle_it	1.931
r_scbond_it	1.19
r_angle_refined_deg	1.012
r_mcangle_it	0.88
r_mcbond_it	0.523
r_nbtor_refined	0.302
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.136
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.074
r_symmetry_hbond_refined	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6604
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	19

Software

Software
Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	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.