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Crystal structure of short chain dehydrogenase MAP_2410 from Mycobacterium paratuberculosis bound to NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PGX pdb entry 3pgx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MypaA.01326.g.A1 PW29476 at 27.6 mg/mL against JCSG+ D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220650d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.98 α = 90 b = 127.17 β = 104.49 c = 69.69 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 ADSC QUANTUM 315r 2011-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 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 2.05 50 98.5 0.13 10.54 4.2 61220 60295 -3 21.616
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 2.05 2.1 97.3 0.474 3.21
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 3pgx 2.05 50 60294 3045 98.56 0.1648 0.1623 0.1636 0.2125 0.2151 RANDOM 14.8272
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] 2.06 0.98 -1.51 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.299 r_dihedral_angle_4_deg 17.393 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 6.197 r_angle_refined_deg 1.495 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7990 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 192
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction