3I8W

Crystal structure of a metallacarborane inhibitor bound to HIV protease


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 292.0
Details 0.1M CAPS pH 10.5, 1.2M Sodium Dihydrogen Phosphate, 0.2M pottasium hydrogen phosphate, 0.2M Lithium Sulphate, final pH 6.0, Cpr=7mg/ml, 5-fold molar inhibitor excess, VAPOR DIFFUSION, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.16 α = 90
b = 92.34 β = 90
c = 48.95 γ = 90
Symmetry
Space Group C 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 -- 2005-10-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.975 APS 19-ID

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
1.7 50 95.4 0.049 -- -- 8.2 19309 14821 0.0 0.0 21.0
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)
1.7 1.76 70.1 0.558 -- 4.3 5.9 --

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 1.7 23.78 0.0 0.0 -- 13436 703 95.3 -- 0.17776 0.17602 0.21192 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 1.7 1.745 -- 30 694 0.243 0.295 -- 67.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.214
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.232
r_scangle_it 2.134
r_xyhbond_nbd_refined 0.131
r_dihedral_angle_3_deg 9.975
r_dihedral_angle_2_deg 41.855
r_scbond_it 1.381
r_symmetry_vdw_refined 0.259
r_gen_planes_refined 0.039
r_angle_refined_deg 3.761
r_mcbond_it 0.664
r_mcangle_it 1.039
r_nbtor_refined 0.323
r_symmetry_hbond_refined 0.183
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 11.972
r_nbd_refined 0.193
r_dihedral_angle_1_deg 5.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 752
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 111

Software

Software
Software Name Purpose
HKL-3000 data collection
MOLREP phasing
REFMAC refinement version: 5.3.0037
HKL-3000 data reduction
HKL-3000 data scaling