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Crystal structure of NAD kinase 1 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U0R PDB ENTRY 1U0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 0.3 M potassium chloride, 50 mM tri-sodium citrate, 15-20% w/v polyethylene glycol 400, 10 mM KI, pH 5.4, VAPOR DIFFUSION, HANGING DROP, pH 5.40
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.612 α = 90 b = 119.017 β = 102.08 c = 67.937 γ = 90
Symmetry Space Group P 1 21 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 2004-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.34 34.37 97.5 0.066 13.9 3.5 42609 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1U0R 2.34 34.37 43681 41254 1330 97.49 0.19607 0.19408 0.2194 0.25696 0.2768 RANDOM 37.698
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] -3.21 0.52 1.71 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 17.786 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_1_deg 9.778 r_scangle_it 2.197 r_scbond_it 1.56 r_angle_refined_deg 1.374 r_angle_other_deg 0.934 r_mcangle_it 0.912 r_mcbond_it 0.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 17.786 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_1_deg 9.778 r_scangle_it 2.197 r_scbond_it 1.56 r_angle_refined_deg 1.374 r_angle_other_deg 0.934 r_mcangle_it 0.912 r_mcbond_it 0.636 r_symmetry_hbond_refined 0.615 r_symmetry_vdw_refined 0.34 r_xyhbond_nbd_refined 0.307 r_symmetry_vdw_other 0.264 r_nbd_other 0.205 r_nbd_refined 0.197 r_nbtor_refined 0.178 r_chiral_restr 0.132 r_mcbond_other 0.116 r_xyhbond_nbd_other 0.113 r_nbtor_other 0.086 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8157 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing