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Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: free+PPi)
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 4 mM cobalt (II) chloride, 4 mM nickel (II) chloride, 4 mM cadmium chloride, 4 mM magnesium chloride, 0.075 M HEPES, pH7.5, 9% PEG 3350, 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.779 α = 90 b = 100.219 β = 90 c = 130.09 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 270 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 2.28 65 100 0.095 0.999 19.3 13.9 24258
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 2.28 2.4 0.697 0.858
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 2.28 65.04 22983 1247 99.97 0.22192 0.22 0.2236 0.25812 0.2607 RANDOM 45.784
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] -0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.103 r_dihedral_angle_4_deg 19.53 r_dihedral_angle_3_deg 17.63 r_dihedral_angle_1_deg 7.256 r_long_range_B_refined 6.231 r_long_range_B_other 6.217 r_mcangle_it 3.422 r_mcangle_other 3.421 r_scangle_other 3.253 r_mcbond_it 1.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.103 r_dihedral_angle_4_deg 19.53 r_dihedral_angle_3_deg 17.63 r_dihedral_angle_1_deg 7.256 r_long_range_B_refined 6.231 r_long_range_B_other 6.217 r_mcangle_it 3.422 r_mcangle_other 3.421 r_scangle_other 3.253 r_mcbond_it 1.972 r_mcbond_other 1.966 r_scbond_it 1.859 r_scbond_other 1.849 r_angle_refined_deg 1.01 r_angle_other_deg 0.99 r_chiral_restr 0.023 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3406 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing