☰ Navigation Tabs
Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GMPPCP and Pantothenate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.4-1.8M trisodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.11 α = 90 b = 103.11 β = 90 c = 91.05 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2009-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.35 40 98.7 0.059 21.2 9.1 23382 54
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 2.35 2.48 94.6 0.502 3.4 8.6 3101
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 2GEV 2.35 34.12 21973 1130 100 0.21666 0.21441 0.2079 0.26286 0.2556 RANDOM 47.35
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] 1.2 0.6 1.2 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.757 r_dihedral_angle_4_deg 19.754 r_dihedral_angle_3_deg 18.103 r_scangle_it 7.551 r_dihedral_angle_1_deg 7.261 r_scbond_it 4.854 r_mcangle_it 3.283 r_mcbond_it 1.87 r_angle_refined_deg 1.406 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.757 r_dihedral_angle_4_deg 19.754 r_dihedral_angle_3_deg 18.103 r_scangle_it 7.551 r_dihedral_angle_1_deg 7.261 r_scbond_it 4.854 r_mcangle_it 3.283 r_mcbond_it 1.87 r_angle_refined_deg 1.406 r_chiral_restr 0.129 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2473 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 101
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling