3BFO

Crystal structure of Ig-like C2-type 2 domain of the human Mucosa-associated lymphoid tissue lymphoma translocation protein 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U2H	PDB entries 1U2H, 2AW2, 1CS6
experimental model	PDB	2AW2	PDB entries 1U2H, 2AW2, 1CS6
experimental model	PDB	1CS6	PDB entries 1U2H, 2AW2, 1CS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1:1 volume ratio of protein solution (50 mg/mL) and reservoir solution (30% PEG MME 550, 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.944	α = 66.5
b = 43.64	β = 90
c = 49.595	γ = 90.02

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 270	Rh coated Si monochromatic mirrors	2007-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91790	CHESS	F1

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	1.15	25	94.6	0.06	22	5.1	103829	103829		-3

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)
	1.15	1.19	91.8		0.651	2.48	3.7	10043

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1U2H, 2AW2, 1CS6	1.15	25	98073	5145	94.57	0.17882	0.17708	0.21182	RANDOM	19.976

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]
0.93	0.17	-0.19	-0.67	0.63	-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.076
r_dihedral_angle_4_deg	23.895
r_dihedral_angle_3_deg	13.739
r_sphericity_free	9.706
r_dihedral_angle_1_deg	7.17
r_sphericity_bonded	6.543
r_scangle_it	5.09
r_scbond_it	4.006
r_mcangle_it	3.337
r_rigid_bond_restr	2.792
r_mcbond_it	2.535
r_angle_refined_deg	1.83
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.226
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.128
r_bond_refined_d	0.017
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3040
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms

Software

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