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The crystal of nucleoside diphosphate kinase from Aspergillus flavus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 2.4M Sodium Citrate, 100mM HEPES, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.836 α = 90 b = 169.47 β = 92.92 c = 146.937 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315r 2014-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.4 33.67 98.86 0.103 49.1 3.6 179636
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.58
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 1NSK 2.4 33.69 170403 8963 98.85 0.22404 0.22167 0.2248 0.268 0.2676 RANDOM 55.111
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] 2.89 -0.43 0.25 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.379 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 18.633 r_long_range_B_refined 11.289 r_long_range_B_other 11.288 r_dihedral_angle_1_deg 8.165 r_scangle_other 7.668 r_mcangle_it 6.776 r_mcangle_other 6.775 r_scbond_it 5.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.379 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 18.633 r_long_range_B_refined 11.289 r_long_range_B_other 11.288 r_dihedral_angle_1_deg 8.165 r_scangle_other 7.668 r_mcangle_it 6.776 r_mcangle_other 6.775 r_scbond_it 5.082 r_scbond_other 5.081 r_mcbond_it 4.662 r_mcbond_other 4.661 r_angle_refined_deg 1.628 r_angle_other_deg 1.239 r_chiral_restr 0.079 r_bond_refined_d 0.008 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 28040 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing