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prenylated FMN synthase from Methanosarcina mazei (MmPFS) in complexed with FMN and DMAP(P)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MmPFS in complexed with FMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M HEPES sodium pH7.5, 5% 2-propanol, 10% polyethylene glycol 4,000, 10% glycerol, 1mM DMAPP
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.66 α = 88.76 b = 95.731 β = 77.756 c = 95.939 γ = 61.692
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 6M 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 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 1.68 48.2 97.2 0.061 0.999 24.1 9.6 323199
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 0.772
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.68 48.196 322254 16161 96.934 0.196 0.1953 0.2027 0.2124 0.2185 RANDOM 40.129
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] -0.001 -0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.954 r_dihedral_angle_3_deg 14.065 r_lrange_other 8.675 r_lrange_it 8.674 r_scangle_it 7.417 r_scangle_other 7.391 r_dihedral_angle_2_deg 6.996 r_dihedral_angle_1_deg 5.938 r_scbond_it 5.074 r_scbond_other 5.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.954 r_dihedral_angle_3_deg 14.065 r_lrange_other 8.675 r_lrange_it 8.674 r_scangle_it 7.417 r_scangle_other 7.391 r_dihedral_angle_2_deg 6.996 r_dihedral_angle_1_deg 5.938 r_scbond_it 5.074 r_scbond_other 5.05 r_mcangle_it 4.628 r_mcangle_other 4.628 r_mcbond_it 3.646 r_mcbond_other 3.645 r_angle_refined_deg 1.637 r_angle_other_deg 0.594 r_symmetry_xyhbond_nbd_refined 0.291 r_nbd_other 0.226 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_47 0.08 r_ncsr_local_group_7 0.079 r_ncsr_local_group_15 0.077 r_ncsr_local_group_55 0.076 r_ncsr_local_group_66 0.076 r_ncsr_local_group_37 0.075 r_ncsr_local_group_5 0.074 r_ncsr_local_group_46 0.074 r_ncsr_local_group_4 0.073 r_ncsr_local_group_32 0.073 r_ncsr_local_group_39 0.073 r_ncsr_local_group_1 0.071 r_ncsr_local_group_29 0.071 r_ncsr_local_group_49 0.071 r_ncsr_local_group_64 0.071 r_ncsr_local_group_40 0.07 r_ncsr_local_group_60 0.07 r_ncsr_local_group_11 0.069 r_ncsr_local_group_34 0.069 r_ncsr_local_group_50 0.069 r_ncsr_local_group_52 0.069 r_ncsr_local_group_62 0.069 r_ncsr_local_group_10 0.068 r_ncsr_local_group_45 0.068 r_ncsr_local_group_21 0.067 r_ncsr_local_group_16 0.066 r_ncsr_local_group_59 0.065 r_ncsr_local_group_13 0.064 r_ncsr_local_group_31 0.064 r_ncsr_local_group_51 0.064 r_ncsr_local_group_43 0.063 r_ncsr_local_group_48 0.063 r_ncsr_local_group_58 0.063 r_ncsr_local_group_18 0.062 r_ncsr_local_group_19 0.062 r_ncsr_local_group_23 0.062 r_ncsr_local_group_24 0.062 r_ncsr_local_group_26 0.062 r_ncsr_local_group_56 0.062 r_ncsr_local_group_57 0.062 r_ncsr_local_group_38 0.061 r_ncsr_local_group_65 0.061 r_ncsr_local_group_20 0.059 r_ncsr_local_group_2 0.058 r_ncsr_local_group_42 0.058 r_ncsr_local_group_8 0.057 r_ncsr_local_group_53 0.057 r_ncsr_local_group_3 0.056 r_ncsr_local_group_12 0.056 r_ncsr_local_group_44 0.056 r_ncsr_local_group_61 0.056 r_ncsr_local_group_9 0.054 r_ncsr_local_group_30 0.054 r_ncsr_local_group_6 0.052 r_ncsr_local_group_25 0.052 r_ncsr_local_group_35 0.051 r_ncsr_local_group_63 0.051 r_ncsr_local_group_22 0.047 r_ncsr_local_group_28 0.047 r_ncsr_local_group_41 0.047 r_ncsr_local_group_14 0.045 r_ncsr_local_group_27 0.044 r_ncsr_local_group_54 0.044 r_ncsr_local_group_17 0.038 r_ncsr_local_group_33 0.035 r_ncsr_local_group_36 0.029 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 16780 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 521
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing