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Apo Wild-type HIV Protease in the open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZ8 pdb entry 2AZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 277 0.2 M Magnesium chloride, 20% w/v PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.416 α = 90 b = 46.416 β = 90 c = 101.37 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD ADSC QUANTUM 210 Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing 2006-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 SSRL BL1-5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 20.8 99 0.057 16.5 6.2 27866 22409 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 98 0.522 3 6.4 1588
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 2AZ8 1.4 20.8 22398 1165 98.68 0.155 0.153 0.1723 0.186 0.2019 RANDOM 15.554
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.646 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 9.025 r_dihedral_angle_1_deg 6.325 r_scangle_it 5.026 r_scbond_it 3.752 r_mcangle_it 2.672 r_mcbond_it 2.151 r_mcbond_other 1.61 r_angle_refined_deg 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.646 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 9.025 r_dihedral_angle_1_deg 6.325 r_scangle_it 5.026 r_scbond_it 3.752 r_mcangle_it 2.672 r_mcbond_it 2.151 r_mcbond_other 1.61 r_angle_refined_deg 1.196 r_angle_other_deg 0.593 r_chiral_restr 0.39 r_symmetry_vdw_other 0.317 r_nbd_refined 0.296 r_symmetry_vdw_refined 0.216 r_nbd_other 0.202 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 760 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction