☰ Navigation Tabs
Crystal structure of pyridoxal kinase from Lactobacillus plantarum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 1.6M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.005 α = 90 b = 69.649 β = 90 c = 132.15 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 315r MIRRORS 2009-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 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 1.3 38.38 99.5 0.076 13.8 7.8 67906 11.01
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 1.3 1.34 98.9 0.298 6.3 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.3 38.38 72366 67906 3607 98.7 0.194 0.194 0.1944 0.202 0.2058 RANDOM 12.47
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 36.551 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_1_deg 5.535 r_scangle_it 2.33 r_scbond_it 1.605 r_angle_refined_deg 1.176 r_mcangle_it 1.109 r_mcbond_it 0.747 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.551 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_1_deg 5.535 r_scangle_it 2.33 r_scbond_it 1.605 r_angle_refined_deg 1.176 r_mcangle_it 1.109 r_mcbond_it 0.747 r_nbtor_refined 0.303 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.072 r_bond_refined_d 0.007 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 2091 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 16
Software Software Software Name Purpose CBASS data collection SHELXS phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling