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Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion SAD MR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M phosphate citrate pH 4.2, crystal tracking ID 216661c1-1MNaI, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.43 α = 90 b = 114.55 β = 92.13 c = 92.77 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944 2010-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 50 99.3 0.132 11.74 7.2 89991 -3 24.921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 91.2 0.531 3.5 6.2 6704
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 SAD WITH MR THROUGHOUT 1jqi 2.1 50 89872 4507 99.18 0.171 0.1691 0.1715 0.2068 0.2094 RANDOM 21.3214
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] -0.57 -0.36 -0.09 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.581 r_dihedral_angle_1_deg 5.346 r_scangle_it 3.262 r_scbond_it 2.033 r_angle_refined_deg 1.393 r_mcangle_it 1.17 r_mcbond_it 0.664 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.581 r_dihedral_angle_1_deg 5.346 r_scangle_it 3.262 r_scbond_it 2.033 r_angle_refined_deg 1.393 r_mcangle_it 1.17 r_mcbond_it 0.664 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10870 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 321
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction