☰ Navigation Tabs
Crystal structure of the adenylation (A) domain of the carboxylate reductase (CAR) GR01_22995 from Mycobacterium chelonae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 20 mg/mL protein, 2.5 mM adipic acid, 1 mM AMP-PNP and the reservoir solution 1.5 M lithium sulfate and 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.34 63.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.325 α = 90 b = 90.58 β = 90 c = 172.202 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 IMAGE PLATE RIGAKU RAXIS IV 2018-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.97 30 98.8 0.058 0.027 30.26 5.8 66954 41.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 81.2 0.743 0.395 0.635 1 4.2
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 5MSD 1.97 29.909 1.34 66873 2000 98.59 0.1835 0.1823 0.1829 0.2241 0.2248 RANDOM
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 20.539 f_angle_d 1.058 f_chiral_restr 0.061 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4957 Nucleic Acid Atoms Solvent Atoms 634 Heterogen Atoms 97
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-2000 data scaling PHENIX phasing PHENIX model building Coot model building