4JLH

HIV-1 Integrase Catalytic Core Domain A128T Mutant Complexed with Allosteric Inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1 M Na Cacodylate, 1.4 M Na Acetate, pH 6.5, Vapor Diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.21 α = 90
b = 72.21 β = 90
c = 65.9 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2013-03-07
Diffraction Radiation
Monochromator Protocol
mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.541 -- --

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
2.09 62.54 99.3 0.034 -- -- 4.0 12121 12058 3.0 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)
2.09 2.13 99.8 0.467 -- -- 3.9 612

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 2.09 50.0 -- 0.0 11420 11995 575 98.96 -- 0.2004 0.1984 0.2429 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 2.09 2.145 -- 48 831 0.271 0.316 -- 99.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.2756
Anisotropic B[1][1] 0.42
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.773
r_scbond_it 2.614
r_bond_refined_d 0.016
r_mcbond_it 0.928
r_mcangle_it 1.779
r_chiral_restr 0.099
r_scangle_it 4.329
r_dihedral_angle_2_deg 33.172
r_dihedral_angle_1_deg 5.396
r_dihedral_angle_4_deg 19.816
r_gen_planes_refined 0.006
r_angle_refined_deg 1.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1090
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 44

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.2.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling