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Crystal structure of cruzain covalently bound to a purine nitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ME3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1 M Tris, 2.0 M NH4H2PO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.967 α = 90 b = 82.967 β = 90 c = 101.895 γ = 120
Symmetry Space Group P 65 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 ADSC QUANTUM 315r 2008-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1
Data Collection Overall ID # 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 1.1 41.48 92.7 0.052 0.052 8.399 11.6 77795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.16 65.1 0.407 0.407 1.9 4.3 7781
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 1ME3 1.1 41.48 77748 3940 92.52 0.12 0.119 0.128 0.142 0.1504 RANDOM 10.649
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] -0.32 -0.16 -0.32 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_4_deg 16.418 r_dihedral_angle_1_deg 12.638 r_sphericity_free 12.4 r_dihedral_angle_3_deg 10.632 r_sphericity_bonded 4.843 r_scangle_it 4.303 r_scbond_it 3.655 r_mcangle_it 2.61 r_mcbond_it 2.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_4_deg 16.418 r_dihedral_angle_1_deg 12.638 r_sphericity_free 12.4 r_dihedral_angle_3_deg 10.632 r_sphericity_bonded 4.843 r_scangle_it 4.303 r_scbond_it 3.655 r_mcangle_it 2.61 r_mcbond_it 2.118 r_angle_refined_deg 2.016 r_rigid_bond_restr 1.804 r_angle_other_deg 1.546 r_mcbond_other 0.871 r_xyhbond_nbd_refined 0.383 r_nbd_refined 0.306 r_symmetry_vdw_other 0.274 r_symmetry_hbond_refined 0.251 r_symmetry_vdw_refined 0.246 r_nbd_other 0.204 r_nbtor_refined 0.184 r_chiral_restr 0.117 r_nbtor_other 0.094 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1696 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 23
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction