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Crystal structure of a Short chain dehydrogenase (A0QTM2 homolog) Mycobacterium thermoresistibile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KVO PDB ENTRY 3KVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Internal tracking number 220646H3. Focus screen based on JCSG E2. 2 M ammonium sulfate, 0.1 M cacodylate, pH 6.54, 200 mM sodium chloride. MythA.01365.a.A1 PW28688 at 27.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.7 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.49 α = 90 b = 111.49 β = 90 c = 124.88 γ = 120
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 ADSC QUANTUM 315 2011-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.5 48.28 99.8 0.101 21.89 9.3 30482 30423 -3 37.017
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 2.5 2.56 100 0.564 4.4 9.2 2240
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 PDB ENTRY 3KVO 2.5 48.28 30393 2343 99.72 0.181 0.178 0.1786 0.22 0.2193 RANDOM 27.608
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] -0.45 -0.22 -0.45 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.398 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 14.984 r_dihedral_angle_1_deg 6.567 r_scangle_it 3.052 r_scbond_it 1.837 r_angle_refined_deg 1.46 r_mcangle_it 1.153 r_angle_other_deg 0.906 r_mcbond_it 0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.398 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 14.984 r_dihedral_angle_1_deg 6.567 r_scangle_it 3.052 r_scbond_it 1.837 r_angle_refined_deg 1.46 r_mcangle_it 1.153 r_angle_other_deg 0.906 r_mcbond_it 0.606 r_mcbond_other 0.122 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4113 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction