☰ Navigation Tabs
THE APO FORM OF E. COLI RIBOKINASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RKD 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 CRYSTALS WERE GROWN IN 22-33% PEG 2000, MONO-METHYLETHER AS PRECIPITANT AND BUFFERED TO PH 4.8 WITH 0.1 M NA ACETATE. CRYO-PROTECTANT: MOTHER LIQUID ALSO CONTAINING 15% ETHYLENEGLYCOL. SOAK-TIME: 2-3 MINUTES.
Crystal Properties Matthews coefficient Solvent content 2.1 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.97 α = 90 b = 61.97 β = 90 c = 127.834 γ = 120
Symmetry Space Group P 31 2 1
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 MIRRORS 1998-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 2.3 15 96.4 0.056 20.6 5.5 12644 32
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 2.3 2.34 87.5 0.235 6.7 5.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309. 2.3 15 12644 12644 619 96.3 0.21 0.2055 0.253 0.2133 RANDOM 27
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] -2.84 -1.66 -2.84 5.685
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.1 x_scangle_it 2.5 x_scbond_it 1.8 x_mcangle_it 1.7 x_angle_deg 1.5 x_mcbond_it 1.1 x_improper_angle_d 0.76 x_bond_d 0.007 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.1 x_scangle_it 2.5 x_scbond_it 1.8 x_mcangle_it 1.7 x_angle_deg 1.5 x_mcbond_it 1.1 x_improper_angle_d 0.76 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling