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Crystal structure of cruzain with gallinamide analog from 2-indolyl series
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 800mM Potassium Phosphate, pH 8.0; 100mM Calcium Chloride; Betaine hydrochloride
Crystal Properties Matthews coefficient Solvent content 4.03 69.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.93 α = 90 b = 95.93 β = 90 c = 68.85 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS3 6M Mirrors 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.08 83.08 98.9 0.42 0.431 0.995 8.37 19.676 22026 42.284
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.14 86.3 5.558 5.721 0.158 0.54 16.594
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3kku 2.08 83.08 20511 1056 96.93 0.2025 0.2002 0.2477 0.2335 RANDOM 39.271
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.871 r_dihedral_angle_4_deg 21.09 r_dihedral_angle_3_deg 16.246 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 2.173 r_angle_other_deg 1.085 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.871 r_dihedral_angle_4_deg 21.09 r_dihedral_angle_3_deg 16.246 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 2.173 r_angle_other_deg 1.085 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1592 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing