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Crystal structure of human neutrophil peptide 2, HNP-2 (variant Gly16-> D-Ala)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DEF BASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 lithium sulfate, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.038 α = 90 b = 26.051 β = 105.79 c = 61.587 γ = 90
Symmetry Space Group P 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 2004-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.48 50 95.6 0.038 20719 20719
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.55 65.3
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF) 1.5 19 19047 19047 1022 95.6 0.179 0.17921 0.17734 0.192 0.21252 0.1995 RANDOM 26.748
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] -0.12 -0.03 0.06 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.474 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 11.783 r_sphericity_free 9.97 r_dihedral_angle_1_deg 7.516 r_sphericity_bonded 5.673 r_scangle_it 4.267 r_mcangle_it 3.976 r_scbond_it 3.276 r_mcbond_it 2.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.474 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 11.783 r_sphericity_free 9.97 r_dihedral_angle_1_deg 7.516 r_sphericity_bonded 5.673 r_scangle_it 4.267 r_mcangle_it 3.976 r_scbond_it 3.276 r_mcbond_it 2.945 r_rigid_bond_restr 2.467 r_angle_refined_deg 2.023 r_symmetry_hbond_refined 0.351 r_nbtor_refined 0.331 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.141 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 936 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing