2IF5 | pdb_00002if5

Structure of the POZ domain of human LRF, a master regulator of oncogenesis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Protein at 24 mg/ml in 25 mM Tris, 150 mM NaCl, 2mM DTT, 0.18 M Calcium acetate hydrate, 18% w/v Polyethylene glycol 3350, 0.01 M Praseodymium (III) Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.85	α = 90
b = 65.85	β = 90
c = 162.603	γ = 90

Symmetry
Space Group	I 41 2 2

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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	50	98.2	0.096	0.096	25.9	13		12540		-1	19.2

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	2.03	2.13	99.8		0.259	0.259	9	13

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BUO	2	40.08	11695	620	98.24	0.23245	0.22933	0.2305	0.29096	0.2929	RANDOM	22.928

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]
0.2			0.2		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.34
r_dihedral_angle_4_deg	20.641
r_dihedral_angle_3_deg	12.921
r_dihedral_angle_1_deg	5.285
r_scangle_it	3.966
r_scbond_it	2.857
r_mcangle_it	1.891
r_angle_refined_deg	1.58
r_mcbond_it	1.198
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.206
r_symmetry_hbond_refined	0.167
r_chiral_restr	0.111
r_metal_ion_refined	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	877
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing