☰ Navigation Tabs
Crystal structure of D235A mutant of human pyridoxal kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXU PDB entry 2YXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 Protein solution: 20 mM Sodium BES buffer pH 7.2, 100 mM NaCl, 5 mM BME, 2.5 mM MgATP, 1 mM PLP. Precipitant: 100 mM Tris-HCl pH 8.0, 57% MPD, 5 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.17 61.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.224 α = 90 b = 115.422 β = 90 c = 168.898 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 IMAGE PLATE RIGAKU RAXIS IV MSC Varimax confocal optics 2008-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 2.5 32.69 99.7 0.083 3.99 31128
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 2.5 2.59 99.6 0.298 4.2 3.79 3079
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 (All) 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 2YXU 2.5 29.93 31124 31124 1568 99.6 0.214 0.214 0.212 0.2059 0.262 0.2544 RANDOM 44.391
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] 17.54 -9 -8.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_improper_angle_d 2.17 c_angle_deg 1.4 c_bond_d 0.008 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4869 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 193
Software Software Software Name Purpose d*TREK data scaling CNS refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction CNS phasing