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Saccharomyces cerevisiae nucleoside diphosphate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUE PDB ENTRY 1nue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 291 13% isopropanol, 19% TBA(tert-butyl alcohol), 0.1M Na Citrate pH 5.6, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.68 66.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.92 α = 90 b = 185.92 β = 90 c = 185.92 γ = 90
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 RIGAKU RAXIS IV++ 2006-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 3 29.4 98.2 0.112 5.6122 6.41 10547 10547
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 3 3.16 93.35 0.7 1.1 4.89
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 MIR THROUGHOUT PDB ENTRY 1nue 3.1 15 8869 431 95.94 0.23221 0.23081 0.2641 0.26081 0.304 RANDOM 60
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.516 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 20.916 r_dihedral_angle_1_deg 8.422 r_scangle_it 2.122 r_angle_refined_deg 1.939 r_scbond_it 1.292 r_mcangle_it 0.802 r_mcbond_it 0.438 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.516 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 20.916 r_dihedral_angle_1_deg 8.422 r_scangle_it 2.122 r_angle_refined_deg 1.939 r_scbond_it 1.292 r_mcangle_it 0.802 r_mcbond_it 0.438 r_nbtor_refined 0.333 r_symmetry_hbond_refined 0.315 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.255 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2290 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling AMoRE phasing