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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
3VAF
Structure of U2AF65 variant with BrU3 DNA
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
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FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
6.5
Temperature
277.0
Details
1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 164.3
α = 90
b = 36.98
β = 125.67
c = 99.43
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315r
--
2005-11-02
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X25
0.960
NSLS
X25
Data Collection
Overall
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
2.49
50
99.3
0.134
--
--
6.6
--
17441
--
-1.0
--
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
2.49
2.58
99.3
0.455
--
--
4.7
1612
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
MOLECULAR REPLACEMENT
2.49
20.51
--
0.0
17997
16380
1617
93.5
--
0.2361
0.2305
0.2886
RANDOM
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
2.486
2.55
--
96
963
0.371
0.459
--
84.79
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
35.2124
Anisotropic B[1][1]
-0.64
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.5
Anisotropic B[2][2]
0.23
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
1.0
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_1_deg
6.179
r_xyhbond_nbd_refined
0.15
r_xyhbond_nbd_other
0.041
r_mcbond_it
0.509
r_angle_other_deg
1.093
r_dihedral_angle_4_deg
16.232
r_nbd_other
0.196
r_symmetry_vdw_refined
0.194
r_gen_planes_refined
0.004
r_gen_planes_other
0.001
r_dihedral_angle_2_deg
35.579
r_symmetry_vdw_other
0.174
r_bond_other_d
0.005
r_chiral_restr
0.096
r_mcangle_it
0.633
r_nbd_refined
0.216
r_bond_refined_d
0.011
r_symmetry_hbond_refined
0.16
r_dihedral_angle_3_deg
16.179
r_scangle_it
1.793
r_angle_refined_deg
1.401
r_scbond_it
1.149
r_nbtor_other
0.086
r_nbtor_refined
0.188
r_mcbond_other
0.082
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2675
Nucleic Acid Atoms
226
Heterogen Atoms
87
Solvent Atoms
119
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
REFMAC
refinement version: 5.2.0019
PDB_EXTRACT
data extraction version: 3.10
HKL-2000
data collection
PHASER
phasing