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Dodecin from Streptomyces davaonensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M (NH4)2SO4, 10% (w/v) PEG-4000, 0.1 M NaOAc, pH 4.8
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.288 α = 90 b = 72.288 β = 90 c = 151.213 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.07 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 100 28 11 16434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 0.54
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2yiz 2.4 36.17 15514 99.96 0.22 0.25 0.2414 RANDOM 41
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_3_deg 16.283 r_dihedral_angle_4_deg 12.573 r_long_range_B_refined 10.011 r_long_range_B_other 10.01 r_dihedral_angle_1_deg 7.569 r_scangle_other 7.216 r_mcangle_it 6.406 r_mcangle_other 6.405 r_scbond_it 4.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_3_deg 16.283 r_dihedral_angle_4_deg 12.573 r_long_range_B_refined 10.011 r_long_range_B_other 10.01 r_dihedral_angle_1_deg 7.569 r_scangle_other 7.216 r_mcangle_it 6.406 r_mcangle_other 6.405 r_scbond_it 4.514 r_scbond_other 4.513 r_mcbond_it 4.004 r_mcbond_other 4.002 r_angle_refined_deg 1.448 r_angle_other_deg 1.275 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3257 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing