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Structure of MA1831 from Methanosarcina acetivorans in complex with farnesyl pyrophosphate and dimethylallyl diphosphate
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, SITTING DROP 8 298 1.5M ammonium sulfate, 0.1M Tris (pH 8.0), 12% glycerol
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.642 α = 90 b = 80.778 β = 103.56 c = 59.806 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 100 PIXEL Bruker PHOTON III 2021-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 1.96 33.04 97.2 0.109 0.121 0.051 0.997 9.7 5.3 33955
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 1.96 2.01 61.1 0.652 0.79 0.433 0.674 2.7
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 7CAQ 2.11 33.04 28321 1468 99.94 0.1562 0.1538 0.1676 0.2017 0.2089 RANDOM 29.892
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] 2.11 -0.45 -0.31 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.472 r_dihedral_angle_4_deg 19.505 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.532 r_angle_other_deg 1.315 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.472 r_dihedral_angle_4_deg 19.505 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.532 r_angle_other_deg 1.315 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3378 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement SAINT data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing