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Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and neridronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KB9 PDB entry 3KB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.05 mM Bis-Tris, pH 5.5, 0.05 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 27% PEG3350, 0.01 M L-Proline
Crystal Properties Matthews coefficient Solvent content 2.04 39.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.53 α = 90 b = 46.76 β = 98.34 c = 74.82 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 9M 2020-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.98 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.4 46.76 99.8 0.994 6.3 3.2 69464 11.37
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 1.4 1.42 0.559
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3KB9 1.4 45.16 1.35 69430 1999 99.77 0.1954 0.1941 0.2391 0.2478 17.09
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.9298 f_angle_d 0.8029 f_chiral_restr 0.069 f_plane_restr 0.0056 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2742 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing