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Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFN Based on monomer of HNP-3 (PDB ID code 1DFN)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 tri-sodium citrate dihydrate, Tris/HCl, PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.148 α = 90 b = 47.148 β = 90 c = 50.643 γ = 90
Symmetry Space Group P 42 21 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 2004-06-10 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 1.1 30 97.7 0.07 15.7 10.2 24405 24405
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 1.1 1.15 89.8 0.429 2.2 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Based on monomer of HNP-3 (PDB ID code 1DFN) 1.3 19.47 13688 734 98.76 0.16116 0.16116 0.16033 0.1931 0.17676 RANDOM 15.779
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 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.488 r_dihedral_angle_3_deg 10.723 r_dihedral_angle_4_deg 10.136 r_sphericity_free 9.842 r_dihedral_angle_1_deg 8.149 r_angle_other_deg 3.881 r_sphericity_bonded 3.526 r_scangle_it 3.38 r_mcangle_it 3.102 r_scbond_it 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.488 r_dihedral_angle_3_deg 10.723 r_dihedral_angle_4_deg 10.136 r_sphericity_free 9.842 r_dihedral_angle_1_deg 8.149 r_angle_other_deg 3.881 r_sphericity_bonded 3.526 r_scangle_it 3.38 r_mcangle_it 3.102 r_scbond_it 3.017 r_mcbond_it 2.553 r_angle_refined_deg 1.721 r_rigid_bond_restr 1.636 r_mcbond_other 1.012 r_symmetry_hbond_refined 0.424 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.288 r_symmetry_vdw_other 0.279 r_xyhbond_nbd_other 0.258 r_xyhbond_nbd_refined 0.245 r_nbd_other 0.235 r_nbtor_refined 0.197 r_chiral_restr 0.183 r_nbtor_other 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 468 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing