5TC2

C-terminal domain of HIV-1 integrase, crystal structure


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.15
Details 2.1M di-Sodium DL-malate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.14 α = 90
b = 72.62 β = 106.39
c = 33.89 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-12-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97858 SOLEIL PROXIMA 1

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
1.84 36.31 98.7 0.112 -- -- 3.2 -- 10034 -- -- 32.8
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)
1.84 1.88 84.2 1.225 -- 0.8 2.1 --

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 1.84 36.31 -- 0.0 -- 9990 517 98.2 -- 0.219 0.218 0.24 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 1.84 2.06 -- 146 2545 0.204 0.236 0.0 93.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.37
Anisotropic B[1][1] -3.0224
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1336
Anisotropic B[2][2] 1.3313
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.6911
RMS Deviations
Key Refinement Restraint Deviation
t_omega_torsion 3.32
t_bond_d 0.008
t_angle_deg 1.1
t_other_torsion 18.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 916
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 48

Software

Software
Software Name Purpose
BUSTER refinement version: 2.10.2
XDS data reduction
Aimless data scaling
MOLREP phasing