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Crystal structure of human alpha-defensin-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFN Based on the monomer of HNP-3 (PDB ID code 1DFN)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 sodium citrate, HEPES, 2-Methyl-2,4-pentanediol, PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.004 α = 90 b = 39.255 β = 110.08 c = 48.118 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 MARRESEARCH 2004-09-20 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 95.2 0.072 12.1 3.3 15948 15948
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 71.1 0.233 3.5 3
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 MOLECULAR REPLACEMENT THROUGHOUT Based on the monomer of HNP-3 (PDB ID code 1DFN) 1.6 15 15127 15127 806 95.2 0.18707 0.18545 0.1957 0.21791 RANDOM 13.366
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 -0.39 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.712 r_scangle_it 2.664 r_mcangle_it 2.283 r_scbond_it 1.686 r_angle_refined_deg 1.615 r_mcbond_it 1.45 r_angle_other_deg 0.697 r_symmetry_vdw_other 0.368 r_symmetry_vdw_refined 0.277 r_xyhbond_nbd_refined 0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.712 r_scangle_it 2.664 r_mcangle_it 2.283 r_scbond_it 1.686 r_angle_refined_deg 1.615 r_mcbond_it 1.45 r_angle_other_deg 0.697 r_symmetry_vdw_other 0.368 r_symmetry_vdw_refined 0.277 r_xyhbond_nbd_refined 0.276 r_nbd_other 0.274 r_symmetry_hbond_refined 0.264 r_nbd_refined 0.223 r_chiral_restr 0.096 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling EPMR phasing