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Simocyclinone C4 bound form of TetR-like repressor SimR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y2Z PDB ENTRY 2Y2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 5MG/ML PLUS EXCESS LIGAND IN 25MM TRIS-HCL PH8.4, 300MM NACL MIXED WITH 28% PEG 400, 0.2M CALCIUM CHLORIDE 0.1M HEPES PH7.5 IN 1 TO 1 RATIO
Crystal Properties Matthews coefficient Solvent content 3.13 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.57 α = 90 b = 86.57 β = 90 c = 349.861 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC CCD 2010-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.3 63.06 97.3 0.11 15.4 8.4 34449 -3 28.8
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 2.3 2.42 98.5 0.37 5.4 8.5
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 2Y2Z 2.3 74.97 32723 1726 96.34 0.20019 0.19776 0.1951 0.24612 0.2455 RANDOM 17
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] -0.67 -0.33 -0.67 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.904 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.37 r_scangle_it 4.369 r_scbond_it 2.657 r_mcangle_it 1.729 r_angle_refined_deg 1.576 r_angle_other_deg 0.926 r_mcbond_it 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.904 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.37 r_scangle_it 4.369 r_scbond_it 2.657 r_mcangle_it 1.729 r_angle_refined_deg 1.576 r_angle_other_deg 0.926 r_mcbond_it 0.912 r_mcbond_other 0.195 r_chiral_restr 0.091 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3748 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing