6NXK

Ubiquitin binding variants


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 277.15
Details 0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.89 α = 90
b = 63.37 β = 90
c = 100.14 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2015-08-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C

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
2.2 53.55 96.5 0.069 0.069 -- 4.4 -- 17815 -- -3.0 --
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)
2.2 2.27 99.0 0.583 0.583 -- 4.4 --

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 2.2 53.55 -- -- -- 17815 980 95.64 -- 0.22287 0.2205 0.2662 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 2.2 2.257 -- 76 1335 0.331 0.308 -- 98.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.829
Anisotropic B[1][1] -3.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.59
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_other 6.109
r_long_range_B_refined 7.585
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 5.924
r_dihedral_angle_2_deg 40.842
r_mcangle_other 3.997
r_dihedral_angle_4_deg 13.741
r_bond_other_d 0.002
r_mcangle_it 3.998
r_mcbond_it 2.708
r_gen_planes_refined 0.005
r_scbond_other 3.756
r_angle_refined_deg 1.34
r_long_range_B_other 7.561
r_bond_refined_d 0.01
r_angle_other_deg 0.898
r_mcbond_other 2.708
r_dihedral_angle_3_deg 15.457
r_chiral_restr 0.074
r_scbond_it 3.757
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2395
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 116

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction
XDS data scaling
PHASER phasing