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Human beta-defensin-1 (Mutant Asn4Ala)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJV PDB entry 1IJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.52 α = 90 b = 26.4 β = 100.8 c = 57.53 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2005-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.85 40 99.9 0.08 17.1 5.2 12053 12053 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 99.6 0.255 6 5 1178
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 PDB entry 1IJV 1.85 30 12045 12045 577 99.77 0.182 0.182 0.179 0.1886 0.238 RANDOM 21.632
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] 0.02 0.84 -0.21 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.744 r_dihedral_angle_4_deg 27.592 r_dihedral_angle_3_deg 13.612 r_dihedral_angle_1_deg 5.506 r_scangle_it 3.169 r_scbond_it 2.23 r_angle_refined_deg 1.523 r_mcangle_it 1.483 r_mcbond_it 1.013 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.744 r_dihedral_angle_4_deg 27.592 r_dihedral_angle_3_deg 13.612 r_dihedral_angle_1_deg 5.506 r_scangle_it 3.169 r_scbond_it 2.23 r_angle_refined_deg 1.523 r_mcangle_it 1.483 r_mcbond_it 1.013 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1072 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 25
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing