☰ Navigation Tabs
Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase from Mycobacterium paratuberculosis in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OEC PDB entry 3oec modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 EBS JCSG+ SCREEN D5 OPTIMIZED TO: 100MM HEPES PH 6.5, 70% MPD; MYPAA.01326.D.A1 PW29473 AT 23MG/ ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.49 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.46 α = 97.01 b = 70.76 β = 93.92 c = 125.68 γ = 86.91
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 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
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 1.5 20 94.8 0.039 21.04 3.8 351856 333445 -3 21.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 90.3 0.304 0.304 4.1 3.5 26062
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MR THROUGHOUT PDB entry 3oec modified with CCP4 program CHAINSAW 1.5 20 351856 333440 16842 94.8 0.141 0.141 0.14 0.1487 0.159 0.1666 RANDOM 11.48
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] -0.11 0.08 0.14 0.01 0.47 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_4_deg 17.173 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 5.893 r_scangle_it 3.531 r_scbond_it 2.22 r_angle_refined_deg 1.711 r_angle_other_deg 1.609 r_mcangle_it 1.419 r_mcbond_it 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_4_deg 17.173 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 5.893 r_scangle_it 3.531 r_scbond_it 2.22 r_angle_refined_deg 1.711 r_angle_other_deg 1.609 r_mcangle_it 1.419 r_mcbond_it 0.844 r_mcbond_other 0.26 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14978 Nucleic Acid Atoms Solvent Atoms 1563 Heterogen Atoms 392
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling