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Human beta-defensin-1 (Mutant GLN24ALA)
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 293 PEG 4000, AMMONIUM SULFATE, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.59 α = 90 b = 26.77 β = 102.6 c = 59.6 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 2005-08-15 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 50 100 0.066 27 7 12097 12097 -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) 1.85 1.92 99.6 0.506 2.8 6.3 1204
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 12083 12083 577 99.87 0.188 0.188 0.185 0.1952 0.243 RANDOM 31.692
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] -0.92 -0.03 0.29 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 20.142 r_dihedral_angle_3_deg 13.891 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.906 r_scbond_it 2.742 r_mcangle_it 1.973 r_angle_refined_deg 1.662 r_mcbond_it 1.265 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 20.142 r_dihedral_angle_3_deg 13.891 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.906 r_scbond_it 2.742 r_mcangle_it 1.973 r_angle_refined_deg 1.662 r_mcbond_it 1.265 r_nbtor_refined 0.3 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing