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Derivative of human alpha-defensin 1 (HNP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2 M sodium citrate, 0.1 M HEPES, 20 (v/v/) iso-Propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.811 α = 90 b = 38.811 β = 90 c = 31.56 γ = 120
Symmetry Space Group P 31 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 CCD MARMOSAIC 300 mm CCD mirrors 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.96 APS 22-BM
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 1.6 30 98.4 0.077 0.077 16.7 3.7 3787 3787 -3
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) 1.6 1.66 98.7 0.405 0.405 2.8 3.6 374
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DFN 1.6 20 3787 3602 168 98.51 0.15363 0.15363 0.15128 0.1531 0.20087 RANDOM 24.406
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.376 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 8.449 r_dihedral_angle_4_deg 7.623 r_sphericity_free 6.687 r_sphericity_bonded 4.295 r_scangle_it 4.149 r_scbond_it 3.92 r_rigid_bond_restr 3.464 r_mcangle_it 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.376 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 8.449 r_dihedral_angle_4_deg 7.623 r_sphericity_free 6.687 r_sphericity_bonded 4.295 r_scangle_it 4.149 r_scbond_it 3.92 r_rigid_bond_restr 3.464 r_mcangle_it 2.686 r_angle_refined_deg 1.959 r_mcbond_it 1.725 r_chiral_restr 0.656 r_symmetry_hbond_refined 0.378 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.283 r_xyhbond_nbd_refined 0.242 r_nbd_refined 0.227 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 226 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing