☰ Navigation Tabs
COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KIF PDB ENTRY 1KIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID
Crystal Properties Matthews coefficient Solvent content 3.48 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 326.4 α = 90 b = 136.9 β = 90 c = 196.5 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 IMAGE PLATE MARRESEARCH 1996-11-02 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 3.2 20 99.8 0.112 5 4 72287 30
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) 3.2 3.25 99.1 0.352 2 4
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION DENSITY AVERAGING PDB ENTRY 1KIF 3.2 20 72287 72287 1000 99 0.232 0.232 0.232 0.2488 0.26
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 t_it 7.103 t_angle_deg 3.35 t_nbd 0.12 t_bond_d 0.02 t_gen_planes 0.016 t_trig_c_planes 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21760 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 464
Software Software Software Name Purpose DM model building TNT refinement DENZO data reduction SCALEPACK data scaling DM phasing