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Crystal structure of human defensin-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimental phases
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 HEPES, lithium sulfate monohydrate, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.12 60.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.375 α = 90 b = 49.375 β = 90 c = 255.185 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 MARRESEARCH 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.9200 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 30 90.2 0.086 22.1 8.7 23239 23239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 50 0.388 2.5 5.6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT Expermiental phases 1.65 19.73 20981 20981 1123 94.37 0.20046 0.19842 0.2239 0.24027 RANDOM 18.213
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 11.736 r_dihedral_angle_1_deg 6.509 r_sphericity_bonded 3.367 r_scangle_it 2.764 r_mcangle_it 2.397 r_rigid_bond_restr 2.187 r_scbond_it 1.842 r_angle_refined_deg 1.643 r_mcbond_it 1.423 r_angle_other_deg 0.702
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 11.736 r_dihedral_angle_1_deg 6.509 r_sphericity_bonded 3.367 r_scangle_it 2.764 r_mcangle_it 2.397 r_rigid_bond_restr 2.187 r_scbond_it 1.842 r_angle_refined_deg 1.643 r_mcbond_it 1.423 r_angle_other_deg 0.702 r_symmetry_vdw_other 0.537 r_nbd_other 0.433 r_symmetry_hbond_refined 0.317 r_symmetry_vdw_refined 0.313 r_xyhbond_nbd_refined 0.291 r_nbtor_other 0.258 r_nbd_refined 0.23 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SHELXD phasing SHARP phasing