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E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121
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 THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4
AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS-
HCL BUFFERED TO PH 4.8.
Crystal Properties Matthews coefficient Solvent content 2.2 33.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.201 α = 90 b = 62.492 β = 90 c = 337.8 γ = 90
Symmetry Space Group P 21 21 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 BENT MIRROR 1998-05-18 M SINGLE WAVELENGTH
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 2.25 13 99.1 0.072 17 4 55979 26
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) 2.25 2.29 98.8 0.291 3.9 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.25 13 55979 2815 99 0.228 0.2118 0.265 0.2157 RANDOM 24.4
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] 1.63 5.01 -6.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_angle_deg 1.4 c_improper_angle_d 0.81 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_angle_deg 1.4 c_improper_angle_d 0.81 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8972 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 172
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling