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Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M MgCl2, 0.1M HEPES pH 6.5, 25% PEG3350, 20mM ATP , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.357 α = 90 b = 69.576 β = 90 c = 132.369 γ = 90
Symmetry Space Group C 2 2 21
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 Mirrors 2009-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A
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 38.46 99.6 0.089 9.9 11 20473 19397 25.7
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) 2 2.05 100 0.293 6.6 8.5 1406
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3H74 2 38.46 1 20473 19397 1056 100 0.17759 0.17531 0.21946 0.2752 RANDOM 17.029
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 37.118 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 6.049 r_scangle_it 4.032 r_scbond_it 2.671 r_mcangle_it 1.641 r_angle_refined_deg 1.633 r_mcbond_it 1.192 r_symmetry_hbond_refined 0.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.118 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 6.049 r_scangle_it 4.032 r_scbond_it 2.671 r_mcangle_it 1.641 r_angle_refined_deg 1.633 r_mcbond_it 1.192 r_symmetry_hbond_refined 0.517 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.295 r_nbd_refined 0.213 r_metal_ion_refined 0.193 r_symmetry_vdw_refined 0.193 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2037 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 32
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling