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Ribokinase from Leishmania donovani with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 296 0.1M Citric acid, 3.4M Sodium chloride, 10mM Magnesium chloride, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.902 α = 90 b = 99.902 β = 90 c = 125.554 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 MARMOSAIC 225 mm CCD 2016-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9794 RRCAT INDUS-2 PX-BL21
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 1.8 46.41 100 0.07 17.9 7.9 65706
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 1.8 1.84 0.824
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FV7 1.8 46.41 62408 3242 99.98 0.18301 0.18175 0.2058 0.2014 RANDOM 30.124
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] -1.4 -0.7 -1.4 4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.506 r_dihedral_angle_4_deg 20.386 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_1_deg 6.716 r_long_range_B_refined 6.287 r_long_range_B_other 6.278 r_scangle_other 4.943 r_mcangle_it 3.439 r_mcangle_other 3.439 r_scbond_it 3.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.506 r_dihedral_angle_4_deg 20.386 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_1_deg 6.716 r_long_range_B_refined 6.287 r_long_range_B_other 6.278 r_scangle_other 4.943 r_mcangle_it 3.439 r_mcangle_other 3.439 r_scbond_it 3.279 r_scbond_other 3.279 r_mcbond_it 2.463 r_mcbond_other 2.462 r_angle_refined_deg 1.569 r_angle_other_deg 0.993 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4870 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing