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Human beta-defensin-1 (Mutant Leu13Glu)
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 4.6 293 PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.01 α = 90 b = 46.79 β = 97.3 c = 28.56 γ = 90
Symmetry Space Group C 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 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2004-12-10 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 1.45 40 99 0.07 18 4.5 13851 13851 -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) 1.45 1.5 97.2 0.189 5.8 3.6 1365
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 1.45 30 13844 13844 988 98.96 0.143 0.143 0.14 0.1369 0.184 RANDOM 13.457
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 0.01 -0.11 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.743 r_dihedral_angle_4_deg 32.131 r_dihedral_angle_3_deg 10.307 r_dihedral_angle_1_deg 6.25 r_scangle_it 4.424 r_scbond_it 3.427 r_mcangle_it 2.512 RIGID-BOND RESTRAINTS (A**2) 1.987 r_mcbond_it 1.871 r_angle_refined_deg 1.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.743 r_dihedral_angle_4_deg 32.131 r_dihedral_angle_3_deg 10.307 r_dihedral_angle_1_deg 6.25 r_scangle_it 4.424 r_scbond_it 3.427 r_mcangle_it 2.512 RIGID-BOND RESTRAINTS (A**2) 1.987 r_mcbond_it 1.871 r_angle_refined_deg 1.672 r_nbtor_refined 0.302 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 SPHERICITY; FREE ATOMS (A**2) SPHERICITY; BONDED ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 574 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 20
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