3VAF | pdb_00003vaf

Structure of U2AF65 variant with BrU3 DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G4B	PDB ENTRY 2G4B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.296	α = 90
b = 36.981	β = 125.67
c = 99.431	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 315r		2005-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.960	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.49	50	99.3	0.134	18.3	6.6		17441		-1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.58	99.3		0.455		4.7	1612

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 2G4B	2.49	20.51	17997	16380	1617	93.5	0.2361	0.2305	0.23	0.2886	0.28	RANDOM	35.2124

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]
-0.64		0.5	0.23		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.579
r_dihedral_angle_4_deg	16.232
r_dihedral_angle_3_deg	16.179
r_dihedral_angle_1_deg	6.179
r_scangle_it	1.793
r_angle_refined_deg	1.401
r_scbond_it	1.149
r_angle_other_deg	1.093
r_mcangle_it	0.633
r_mcbond_it	0.509
r_nbd_refined	0.216
r_nbd_other	0.196
r_symmetry_vdw_refined	0.194
r_nbtor_refined	0.188
r_symmetry_vdw_other	0.174
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.096
r_nbtor_other	0.086
r_mcbond_other	0.082
r_xyhbond_nbd_other	0.041
r_bond_refined_d	0.011
r_bond_other_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2675
Nucleic Acid Atoms	226
Solvent Atoms	119
Heterogen Atoms	87

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing