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Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG)
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
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.048 α = 90 b = 99.221 β = 90 c = 193.876 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) R Merge I (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 1.72 48.5 100 0.052 1 42.6 22.3 202517
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 1.72 1.75 1.84 0.672
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7CAQ 1.72 48.062 202517 9998 99.64 0.197 0.1963 0.2129 0.1997 32.316
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] 0.01 -0.024 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.758 r_dihedral_angle_4_deg 18.884 r_dihedral_angle_3_deg 13.63 r_dihedral_angle_1_deg 6.184 r_lrange_it 5.017 r_lrange_other 4.988 r_scangle_it 3.095 r_scangle_other 3.095 r_mcangle_it 2.569 r_mcangle_other 2.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.758 r_dihedral_angle_4_deg 18.884 r_dihedral_angle_3_deg 13.63 r_dihedral_angle_1_deg 6.184 r_lrange_it 5.017 r_lrange_other 4.988 r_scangle_it 3.095 r_scangle_other 3.095 r_mcangle_it 2.569 r_mcangle_other 2.569 r_scbond_it 1.976 r_scbond_other 1.976 r_mcbond_it 1.712 r_mcbond_other 1.712 r_angle_other_deg 1.297 r_angle_refined_deg 1.252 r_nbd_refined 0.192 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.142 r_nbd_other 0.137 r_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.095 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13859 Nucleic Acid Atoms Solvent Atoms 781 Heterogen Atoms 556
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing