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Molybdopterin biosynthesis MoaE protein from Burkholderia ambifaria MC40-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QIE pdb entry 2qie as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1.PS37913 at 49.6 mg/ml + 0.5% n-Octyl-??-D-glucopyranoside: cryo: direct: tray 317329b5, puck xxu3-9
Crystal Properties Matthews coefficient Solvent content 3.08 60.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.68 α = 90 b = 93.29 β = 90.103 c = 65.25 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 CCD RAYONIX MX-300 Beryllium Lenses 2020-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.9 50 98.8 0.048 0.056 0.999 16.26 3.672 52076 37.499
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 87.4 0.392 0.474 0.915 3.04 2.991
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE pdb entry 2qie as per Morda 1.9 48.25 1.36 52055 1986 98.76 0.1801 0.1792 0.18 0.2031 0.204 0 41.9
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.3228 f_angle_d 0.8472 f_chiral_restr 0.0607 f_plane_restr 0.0083 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3279 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building