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X-ray Crystal Structure of L-Plectasin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E7R PDB ENTRY 3E7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 292 0.1 M HEPES, 0.2 M ammonium acetate, 21% PEG 3350., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.919 α = 90 b = 53.919 β = 90 c = 21.964 γ = 120
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 2007-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.35 50 99.1 0.076 23.3 8.7 15193
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) 1.35 1.4 97 0.428 5.2 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3E7R 1.35 23.35 7731 396 99.2 0.158 0.157 0.16 0.182 0.1844 RANDOM 26.49
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.162 r_dihedral_angle_3_deg 12.188 r_rigid_bond_restr 10.258 r_scangle_it 9.688 r_scbond_it 9.358 r_sphericity_free 9.321 r_sphericity_bonded 7.357 r_dihedral_angle_1_deg 5.172 r_mcangle_it 3.84 r_mcbond_it 2.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.162 r_dihedral_angle_3_deg 12.188 r_rigid_bond_restr 10.258 r_scangle_it 9.688 r_scbond_it 9.358 r_sphericity_free 9.321 r_sphericity_bonded 7.357 r_dihedral_angle_1_deg 5.172 r_mcangle_it 3.84 r_mcbond_it 2.807 r_angle_refined_deg 1.737 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.314 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 305 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing