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Structure of digestive procathepsin L 3 of Tenebrio molitor larval midgut
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O6X PDB entry 2O6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 0.1 M sodium citrate, 0.2 M ammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.634 α = 90 b = 89.322 β = 92.5 c = 70.076 γ = 90
Symmetry Space Group C 1 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 100 CCD MAR CCD 165 mm 2008-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.42 LNLS D03B-MX1
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 2.11 35 99.3 0.07 25.22 6 20295
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 2.11 2.19 94.7 0.215 6.94 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2O6X 2.11 26.23 19255 19255 1037 99.33 0.16042 0.16042 0.15815 0.163 0.20142 0.2054 RANDOM 35.274
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.283 r_dihedral_angle_4_deg 20.749 r_dihedral_angle_3_deg 14.242 r_dihedral_angle_1_deg 5.686 r_scangle_it 2.181 r_scbond_it 1.578 r_angle_refined_deg 1.282 r_mcangle_it 1.112 r_mcbond_it 0.636 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.283 r_dihedral_angle_4_deg 20.749 r_dihedral_angle_3_deg 14.242 r_dihedral_angle_1_deg 5.686 r_scangle_it 2.181 r_scbond_it 1.578 r_angle_refined_deg 1.282 r_mcangle_it 1.112 r_mcbond_it 0.636 r_nbtor_refined 0.324 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 2362 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 134
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling