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Human alpha-defensin 1 derivative (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 5.6 293 0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.409 α = 90 b = 57.409 β = 90 c = 96.967 γ = 90
Symmetry Space Group P 42 2 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2007-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.4 30 91.1 0.06 0.06 31.2 9.4 6220 6220 -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 2.4 2.49 53.8 0.518 0.518 2.1 4.9 351
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 2.4 20 5868 5868 284 90.71 0.20106 0.20106 0.20024 0.1886 0.21789 RANDOM 63.758
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] 3.25 3.25 -6.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_3_deg 19.234 r_dihedral_angle_1_deg 8.228 r_dihedral_angle_4_deg 7.618 r_scangle_it 2.214 r_angle_refined_deg 1.74 r_scbond_it 1.549 r_mcangle_it 1.354 r_mcbond_it 0.727 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_3_deg 19.234 r_dihedral_angle_1_deg 8.228 r_dihedral_angle_4_deg 7.618 r_scangle_it 2.214 r_angle_refined_deg 1.74 r_scbond_it 1.549 r_mcangle_it 1.354 r_mcbond_it 0.727 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.289 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.216 r_symmetry_vdw_refined 0.212 r_chiral_restr 0.138 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 464 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing