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Crystal structure of a metallacarborane inhibitor bound to HIV protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTZ PDB entry 1ZTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 292 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 Properties Matthews coefficient Solvent content 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.158 α = 90 b = 92.343 β = 90 c = 48.952 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD SBC-3 2005-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.975 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 50 95.4 0.049 55.87 8.2 19309 14821 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 70.1 0.558 4.3 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ZTZ 1.7 23.78 13436 703 95.3 0.17776 0.17602 0.178 0.21192 0.2141 RANDOM 39.214
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.06 0.09 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.855 r_dihedral_angle_4_deg 11.972 r_dihedral_angle_3_deg 9.975 r_dihedral_angle_1_deg 5.081 r_angle_refined_deg 3.761 r_scangle_it 2.134 r_scbond_it 1.381 r_mcangle_it 1.039 r_mcbond_it 0.664 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.855 r_dihedral_angle_4_deg 11.972 r_dihedral_angle_3_deg 9.975 r_dihedral_angle_1_deg 5.081 r_angle_refined_deg 3.761 r_scangle_it 2.134 r_scbond_it 1.381 r_mcangle_it 1.039 r_mcbond_it 0.664 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.259 r_chiral_restr 0.232 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.131 r_gen_planes_refined 0.039 r_bond_refined_d 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 752 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 30
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling