2FYI

Crystal Structure of the Cofactor-Binding Domain of the Cbl Transcriptional Regulator

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AL3	PDB ENTRY 1AL3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	292	3.8 M NaCl, 10 mM Adenosine 5'-Phosphosulphate, 0.1M Hepes, pH 7.50, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
5.09	75.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.686	α = 90
b = 242.373	β = 90
c = 101.626	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARRESEARCH	TRIANGULAR MONOCHROMATOR, BENT MIRROR	2004-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	2.8	30	99.6	0.124	0.092	10.4	3.9		51701		-1.5	39.6

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	2.8	2.9	97.6		0.566	0.639	2.4	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1AL3	2.8	30	49173	46596	2577	99.7	0.187	0.184	0.19	0.226	0.18	RANDOM	39.6

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]
-1.98			2.4		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.309
r_dihedral_angle_3_deg	19.774
r_dihedral_angle_4_deg	19.567
r_dihedral_angle_1_deg	9.055
r_mcangle_it	2.232
r_scangle_it	2.133
r_angle_refined_deg	1.803
r_scbond_it	1.266
r_mcbond_it	1.261
r_nbtor_refined	0.337
r_symmetry_hbond_refined	0.301
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.214
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7125
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing