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Neryl diphosphate synthase from Solanum lycopersicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 PEG 3350, DL-malic acid
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.643 α = 90 b = 49.464 β = 91.21 c = 119.494 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 9M 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
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 1.94 50 99.3 0.32 0.351 0.205 0.929 5.61 3.16 83643
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 1.94 2.05 98.9 1.405 1.556 0.929 0.523 1.07 2.99
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 5HXT 1.94 49.36 40769 2260 99.91 0.20298 0.19999 0.2109 0.25502 0.2635 RANDOM 48.375
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] -2.31 1.24 4.42 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.378 r_dihedral_angle_3_deg 17.049 r_dihedral_angle_4_deg 14.345 r_long_range_B_refined 9.711 r_long_range_B_other 9.692 r_scangle_other 7.242 r_dihedral_angle_1_deg 6.654 r_mcangle_it 5.347 r_mcangle_other 5.347 r_scbond_it 4.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.378 r_dihedral_angle_3_deg 17.049 r_dihedral_angle_4_deg 14.345 r_long_range_B_refined 9.711 r_long_range_B_other 9.692 r_scangle_other 7.242 r_dihedral_angle_1_deg 6.654 r_mcangle_it 5.347 r_mcangle_other 5.347 r_scbond_it 4.731 r_scbond_other 4.729 r_mcbond_it 3.695 r_mcbond_other 3.694 r_angle_refined_deg 1.509 r_angle_other_deg 1.273 r_chiral_restr 0.072 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 3819 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling MOLREP phasing