6EX9

Crystal Structure of HIV-1 Integrase Catalytic Core Domain with Inhibitor Peptide


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 293.0
Details 0.1 M Succinic acid, 15 % w/v PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.52 α = 90
b = 96.52 β = 90
c = 48.49 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2016-02-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97933 ESRF ID23-1

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
2.01 68.26 99.97 0.061 -- -- 9.7 -- 15682 -- -- --
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)
2.014 2.086 99.93 0.885 -- 2.6 -- --

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 2.014 68.249 -- 1.35 -- 15679 810 99.97 -- 0.2284 0.2256 0.2793 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 2.014 2.1402 -- 120 2431 0.3422 0.3686 -- 100.0
X Ray Diffraction 2.1402 2.3054 -- 123 2443 0.293 0.3364 -- 100.0
X Ray Diffraction 2.3054 2.5374 -- 153 2420 0.2623 0.2956 -- 100.0
X Ray Diffraction 2.5374 2.9046 -- 124 2465 0.2549 0.3252 -- 100.0
X Ray Diffraction 2.9046 3.6595 -- 136 2481 0.2338 0.2776 -- 100.0
X Ray Diffraction 3.6595 68.2883 -- 154 2629 0.189 0.2544 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.052
f_dihedral_angle_d 3.04
f_plane_restr 0.006
f_angle_d 0.841
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 51

Software

Software
Software Name Purpose
PHENIX refinement version: (1.11.1_2575: ???)
MOSFLM data reduction
Aimless data scaling
REFMAC phasing