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Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 DL-malic acid, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.31 α = 90 b = 49.23 β = 91.067 c = 121.39 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 2021-10-01 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) 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 1.92 50 100 0.994 9.7 11.7 44740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.04 100 3.1 0.771 1.07 12
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VPC 1.92 49.146 44740 2237 99.989 0.221 0.219 0.229 0.2566 0.2621 49.366
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] -2.084 0.056 5.321 -3.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.347 r_dihedral_angle_6_deg 17.857 r_lrange_it 6.731 r_lrange_other 6.729 r_scangle_it 5.744 r_scangle_other 5.743 r_dihedral_angle_1_deg 5.725 r_dihedral_angle_2_deg 5.549 r_scbond_it 4.086 r_scbond_other 4.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.347 r_dihedral_angle_6_deg 17.857 r_lrange_it 6.731 r_lrange_other 6.729 r_scangle_it 5.744 r_scangle_other 5.743 r_dihedral_angle_1_deg 5.725 r_dihedral_angle_2_deg 5.549 r_scbond_it 4.086 r_scbond_other 4.085 r_mcangle_other 3.892 r_mcangle_it 3.89 r_mcbond_it 2.846 r_mcbond_other 2.846 r_angle_refined_deg 1.566 r_angle_other_deg 0.735 r_nbd_other 0.267 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.22 r_symmetry_nbd_other 0.22 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_metal_ion_refined 0.043 r_symmetry_xyhbond_nbd_refined 0.035 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_other_2_deg 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3778 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction XDS data scaling PHASER phasing