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Crystal structure of LmNADK1 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I2A PDB ENTRY 2I2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP, pH 5.40
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.243 α = 90 b = 74.565 β = 90 c = 118.29 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 315 2005-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.1 30.99 99.9 0.082 18.1 5.5 15878 28.6
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 2.1 2.21 100 0.488 2.9 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I2A 2.1 30.99 16709 15878 831 99.9 0.204 0.203 0.231 0.2577 RANDOM 22.04
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] 1.15 2.09 -3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_4_deg 13.619 r_dihedral_angle_1_deg 9.63 r_angle_refined_deg 1.342 r_scangle_it 1.296 r_scbond_it 0.98 r_mcangle_it 0.731 r_xyhbond_nbd_refined 0.525 r_mcbond_it 0.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_4_deg 13.619 r_dihedral_angle_1_deg 9.63 r_angle_refined_deg 1.342 r_scangle_it 1.296 r_scbond_it 0.98 r_mcangle_it 0.731 r_xyhbond_nbd_refined 0.525 r_mcbond_it 0.461 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.203 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.171 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1995 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing