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Binary complex of a 7S-cis-cis-nepetalactol cyclase from Nepeta mussinii with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.921 α = 90 b = 107.75 β = 104.26 c = 69.361 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 PILATUS3 6M 2017-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 47.16 98.6 0.09 0.097 0.037 0.999 11.2 6.9 175909 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 97 1.564 1.69 0.637 0.561 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2BGK 1.4 47.16 167049 8822 98.51 0.1513 0.1505 0.1682 0.1674 RANDOM 18.4
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] 0.71 0.02 -0.33 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.919 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 5.601 r_angle_refined_deg 1.562 r_angle_other_deg 0.945 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7529 Nucleic Acid Atoms Solvent Atoms 1109 Heterogen Atoms 184
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing