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Crystal structure of Leishmania nucleoside diphosphate kinase b with unordered nucleotide-binding loop.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NSK PDB entry: 1NSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 sodium/potassium phosphate, pH pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.769 α = 90 b = 120.769 β = 90 c = 64.892 γ = 120
Symmetry Space Group P 63 2 2
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 2010-03-10 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 2.95 104.59 98 0.086 11.2 6148
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 2.95 3.06 86.5 0.347 4.5 7
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: 1NSK 2.95 104.59 5850 284 97.92 0.25731 0.25288 0.2473 0.3505 0.3388 RANDOM 63.55
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] 3.9 1.95 3.9 -5.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_4_deg 24.341 r_dihedral_angle_3_deg 23.898 r_dihedral_angle_1_deg 8.425 r_scangle_it 5.74 r_scbond_it 3.351 r_angle_refined_deg 2.572 r_mcangle_it 2.502 r_mcbond_it 1.314 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_4_deg 24.341 r_dihedral_angle_3_deg 23.898 r_dihedral_angle_1_deg 8.425 r_scangle_it 5.74 r_scbond_it 3.351 r_angle_refined_deg 2.572 r_mcangle_it 2.502 r_mcbond_it 1.314 r_chiral_restr 0.143 r_bond_refined_d 0.029 r_gen_planes_refined 0.009 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 896 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 5
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling