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Structure of Leishmania nucleoside diphosphate kinase b with ordered nucleotide-binding loop
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 sodium/potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.58 65.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.371 α = 90 b = 114.371 β = 90 c = 94.84 γ = 120
Symmetry Space Group P 32 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 CCD MARMOSAIC 225 mm CCD 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
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 99 98.9 0.068 5.3 65810
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 1.86 91.9 0.342 3.7 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 99 62422 3348 98.79 0.18081 0.17918 0.1736 0.21145 0.2013 RANDOM 26.693
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] -1.28 -0.64 -1.28 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_4_deg 21.03 r_dihedral_angle_3_deg 13.405 r_dihedral_angle_1_deg 5.604 r_scangle_it 4.859 r_scbond_it 3.006 r_mcangle_it 1.807 r_angle_refined_deg 1.543 r_mcbond_it 0.98 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_4_deg 21.03 r_dihedral_angle_3_deg 13.405 r_dihedral_angle_1_deg 5.604 r_scangle_it 4.859 r_scbond_it 3.006 r_mcangle_it 1.807 r_angle_refined_deg 1.543 r_mcbond_it 0.98 r_chiral_restr 0.122 r_bond_refined_d 0.017 r_gen_planes_refined 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 3511 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 23
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling