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Crystal structure of wild-type onconase with resolution 1.46 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONC PDB ENTRY 1ONC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 34 % PEG 8000, 0.2 Li2(SO4), 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.23 α = 90 b = 38.679 β = 90 c = 69.588 γ = 90
Symmetry Space Group P 21 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 110 CCD OXFORD ATLAS CCD 2009-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.5418
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 1.46 14.23 97.9 0.072 10.8 2.7 41023 15415 6.5
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) 1.46 1.54 86.7 0.342 2.9 1.8 1943
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 (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 1ONC 1.46 14.23 14591 14591 783 98 0.15206 0.14963 0.1493 0.19876 0.1959 RANDOM 7.9
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 33.8 r_dihedral_angle_4_deg 25.089 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 7.138 r_scangle_it 3.49 r_scbond_it 2.512 r_angle_refined_deg 1.818 r_mcangle_it 1.464 r_mcbond_it 1.05 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.8 r_dihedral_angle_4_deg 25.089 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 7.138 r_scangle_it 3.49 r_scbond_it 2.512 r_angle_refined_deg 1.818 r_mcangle_it 1.464 r_mcbond_it 1.05 r_nbtor_refined 0.316 r_xyhbond_nbd_refined 0.262 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.195 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 826 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 19
Software Software Software Name Purpose CrysalisPro data collection PHASER phasing REFMAC refinement CrysalisPro data reduction SCALA data scaling