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Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP
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 PEG3350, DL-Malic acid
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.26 α = 90 b = 50.27 β = 91.327 c = 120.25 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) Rrim 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 1.98 50 100 0.124 0.993 8.52 6.6 41220
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 1.98 2.08 100 2.65 0.75 1.05 6.8
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 1.98 49.165 41220 2061 99.944 0.224 0.2213 0.2343 0.2744 0.2863 64.711
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] -2.42 0.624 7.077 -4.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.413 r_dihedral_angle_6_deg 15.29 r_lrange_other 11.086 r_lrange_it 11.084 r_scangle_it 9.083 r_scangle_other 9.082 r_mcangle_it 6.969 r_mcangle_other 6.969 r_dihedral_angle_2_deg 6.061 r_dihedral_angle_1_deg 6.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.413 r_dihedral_angle_6_deg 15.29 r_lrange_other 11.086 r_lrange_it 11.084 r_scangle_it 9.083 r_scangle_other 9.082 r_mcangle_it 6.969 r_mcangle_other 6.969 r_dihedral_angle_2_deg 6.061 r_dihedral_angle_1_deg 6.016 r_scbond_it 5.953 r_scbond_other 5.952 r_mcbond_it 4.948 r_mcbond_other 4.947 r_angle_refined_deg 1.471 r_angle_other_deg 0.745 r_symmetry_nbd_refined 0.43 r_nbd_other 0.271 r_nbd_refined 0.228 r_symmetry_nbd_other 0.216 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.141 r_ncsr_local_group_1 0.137 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.068 r_metal_ion_refined 0.038 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3818 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction XDS data scaling PHASER phasing