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Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 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 code 1DFN)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 lithium sulfate, PEG8000, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.685 α = 90 b = 71.685 β = 90 c = 54.882 γ = 120
Symmetry Space Group P 32 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 2004-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 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 1.15 30 98.5 0.09 17 8.4 57187 57187
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 1.15 1.22 90.4 0.513 2.4 4.4
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 monomer of HNP-3 (PDB code 1DFN) 1.15 12 54227 54227 2891 98.53 0.16876 0.16807 0.2041 0.18202 RANDOM 14.858
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.987 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 12.241 r_sphericity_free 9.57 r_dihedral_angle_1_deg 8.025 r_scangle_it 3.785 r_sphericity_bonded 3.721 r_scbond_it 3.02 r_mcangle_it 2.887 r_mcbond_it 2.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.987 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 12.241 r_sphericity_free 9.57 r_dihedral_angle_1_deg 8.025 r_scangle_it 3.785 r_sphericity_bonded 3.721 r_scbond_it 3.02 r_mcangle_it 2.887 r_mcbond_it 2.198 r_angle_refined_deg 1.89 r_angle_other_deg 1.84 r_rigid_bond_restr 1.659 r_mcbond_other 1.116 r_chiral_restr 0.413 r_symmetry_vdw_refined 0.3 r_symmetry_vdw_other 0.285 r_nbd_other 0.239 r_xyhbond_nbd_refined 0.223 r_nbtor_refined 0.201 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.194 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.06 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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 936 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing