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Crystal structure of the adenylation domain of CmnG in complex with AMPCPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.8 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0.
Crystal Properties Matthews coefficient Solvent content 1.91 35.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.932 α = 90 b = 78.097 β = 90 c = 82.211 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 CCD RAYONIX MX300-HS 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 30 99.3 0.975 30.125 7.7 32099
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 1.94 2.02 94.2 0.885 2.93 6.1
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 7XBU 1.94 19.94 29321 1546 95.42 0.1858 0.1837 0.192 0.2246 0.2329 RANDOM 21.558
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] 0.5 -0.36 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.876 r_dihedral_angle_4_deg 17.552 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 1.308 r_angle_other_deg 1.241 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.876 r_dihedral_angle_4_deg 17.552 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 1.308 r_angle_other_deg 1.241 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3170 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing