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Crystal structure of MoaB2 protein from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RFQ Crystal structure of Pterin-4-alpha-carbinolamine dehydratase MoaB2 from Mycobacterium marinum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.2M calcium chloride, 14% w/v PEG 400, 0.1M sodium-HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.45 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.295 α = 90 b = 105.56 β = 90 c = 106.913 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 EIGER2 X CdTe 16M Toroidal mirror 2020-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.53 47.69 99.9 0.136 0.141 0.038 0.999 15 13.4 35068
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 2.53 2.64 99.5 0.868 0.902 0.242 0.872 13.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3RFQ 2.53 47.69 33188 1827 99.8 0.19547 0.19187 0.2604 0.2409 RANDOM 49.976
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] 0.08 -0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.239 r_long_range_B_refined 9.382 r_long_range_B_other 9.382 r_dihedral_angle_2_deg 8.141 r_scangle_other 7.785 r_dihedral_angle_1_deg 7.49 r_mcangle_it 6.46 r_mcangle_other 6.459 r_scbond_it 5.248 r_scbond_other 5.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.239 r_long_range_B_refined 9.382 r_long_range_B_other 9.382 r_dihedral_angle_2_deg 8.141 r_scangle_other 7.785 r_dihedral_angle_1_deg 7.49 r_mcangle_it 6.46 r_mcangle_other 6.459 r_scbond_it 5.248 r_scbond_other 5.247 r_mcbond_it 4.493 r_mcbond_other 4.492 r_angle_refined_deg 1.485 r_angle_other_deg 0.499 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6260 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing