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Crystal structure of a Rv0851c ortholog short chain dehydrogenase from Mycobacterium paratuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IOY PDB ENTRY 3IOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MypaA.01097.i.A1 PW29443 at 32.8 mg/mL with full tag against JCSG+ screen condition A5: 0.2 M Mg formate, 20% PEG3350, with 15% ethylene glycol as cryo-protectant, crystal tracking ID 222227a5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.11 α = 90 b = 130.37 β = 90 c = 55.42 γ = 90
Symmetry Space Group P 21 21 2
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 315r 2011-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9791750 APS 19-ID
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 1.6 50 99 0.032 27.39 3.7 71659 70936 -3 19.407
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 1.6 1.64 99.8 0.131 8.22 3.5 5222
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 3IOY 1.6 50 70935 3590 98.99 0.1662 0.1651 0.1655 0.1858 0.1862 RANDOM 13.3916
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] -0.41 -0.27 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 19.313 r_dihedral_angle_3_deg 11.35 r_dihedral_angle_1_deg 5.294 r_angle_refined_deg 1.603 r_chiral_restr 0.278 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3870 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction EPICS-based data collection XDS data reduction