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Crystal structure of the cysteine protease inhibitor, EhICP2, from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NNR PDB ENTRY 2NNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294.15 0.2M Lithium sulfate; 30% PEG4000; 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 294.15K
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.523 α = 90 b = 60.122 β = 90 c = 61.35 γ = 90
Symmetry Space Group P 2 21 21
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 MARMOSAIC 300 mm CCD 2009-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 1.65 28.262 99.3 0.053 23.3 8.8 25606 25606 1.12 1.12 16.9
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 1.65 1.74 98.6 0.162 10.3 8.9 3652
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2NNR 1.65 27.324 1.58 25579 25579 1285 99.11 0.185 0.185 0.183 0.1783 0.214 0.2094 RANDOM 25.184
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] 2.257 -0.308 -1.949
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.901 f_angle_d 1.099 f_chiral_restr 0.075 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1667 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 28
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection