☰ Navigation Tabs
Variant C89S of Dieckmann cyclase, NcmC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 282 1.7 M ammonium sulfate, 2.5% PEG 400, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.361 α = 90 b = 80.361 β = 90 c = 78.323 γ = 90
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 2016-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.55 80.36 99.4 0.089 16.8 11.8 71503
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 1.552 1.557 1.141
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 6E6Y 1.55 80.36 67900 3570 99.4 0.17518 0.17318 0.1874 0.21508 0.2263 RANDOM 23.98
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 12.879 r_long_range_B_refined 8.421 r_long_range_B_other 7.465 r_dihedral_angle_1_deg 5.916 r_scangle_other 5.092 r_scbond_it 3.477 r_scbond_other 3.461 r_mcangle_other 3.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 12.879 r_long_range_B_refined 8.421 r_long_range_B_other 7.465 r_dihedral_angle_1_deg 5.916 r_scangle_other 5.092 r_scbond_it 3.477 r_scbond_other 3.461 r_mcangle_other 3.241 r_mcangle_it 3.24 r_mcbond_it 2.322 r_mcbond_other 2.32 r_angle_refined_deg 2.084 r_angle_other_deg 1.158 r_chiral_restr 0.139 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3936 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing