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Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CAQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol, 3 mM farnesyl pyrophosphate (FPP), 0.3 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.853 α = 90 b = 98.91 β = 90 c = 193.853 γ = 90
Symmetry Space Group P 21 21 21
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 S 6M 2018-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.91 48.46 100 0.688 33.6 22.3 147512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.94 2.05 0.688
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 7CAQ 1.91 47.92 147470 7541 99.814 0.197 0.1963 0.2045 0.2195 0.2262 42.591
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] 0.005 0.007 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.609 r_dihedral_angle_4_deg 20.898 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.388 r_lrange_it 6.197 r_lrange_other 6.185 r_scangle_it 4.317 r_scangle_other 4.3 r_mcangle_it 3.559 r_mcangle_other 3.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.609 r_dihedral_angle_4_deg 20.898 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.388 r_lrange_it 6.197 r_lrange_other 6.185 r_scangle_it 4.317 r_scangle_other 4.3 r_mcangle_it 3.559 r_mcangle_other 3.559 r_scbond_it 2.877 r_scbond_other 2.844 r_mcbond_it 2.581 r_mcbond_other 2.581 r_angle_other_deg 2.263 r_angle_refined_deg 1.306 r_symmetry_nbd_other 0.219 r_nbd_other 0.201 r_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.125 r_symmetry_xyhbond_nbd_other 0.071 r_chiral_restr 0.063 r_symmetry_nbtor_other 0.062 r_metal_ion_refined 0.055 r_bond_other_d 0.034 r_gen_planes_other 0.007 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13896 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing