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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 7.5 293 ISO-PROPANOL, SODIUM CITRATE, HEPES-NA, pH 7.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 32.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.81 α = 90 b = 20.32 β = 90 c = 75.12 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD 2005-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97947 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 0.98 30 95.2 0.072 27 6.1 16514 16514 -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) 0.98 1.02 69.5 0.209 2.7 1180
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 0.98 30 16460 16460 829 95.18 0.106 0.106 0.105 0.1065 0.124 RANDOM 6.976
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] 0.17 0.1 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.156 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_4_deg 10.516 r_dihedral_angle_1_deg 6.829 r_scangle_it 3.86 r_scbond_it 3.158 r_mcangle_it 2.213 r_mcbond_it 1.899 r_angle_refined_deg 1.821 RIGID-BOND RESTRAINTS (A**2) 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.156 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_4_deg 10.516 r_dihedral_angle_1_deg 6.829 r_scangle_it 3.86 r_scbond_it 3.158 r_mcangle_it 2.213 r_mcbond_it 1.899 r_angle_refined_deg 1.821 RIGID-BOND RESTRAINTS (A**2) 1.42 r_angle_other_deg 1.031 MAIN-CHAIN BOND OTHER ATOMS (A**2) 0.699 r_nbd_refined 0.22 r_symmetry_vdw_other 0.214 r_symmetry_hbond_refined 0.203 r_nbtor_refined 0.184 r_nbd_other 0.18 r_chiral_restr 0.177 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.087 r_nbtor_other 0.08 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 SPHERICITY; FREE ATOMS (A**2) SPHERICITY; BONDED ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 273 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
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 AMoRE phasing