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Crystal structure of a putative Ribokinase in complex with ADP from E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H49 PDB ENTRY 3H49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 292 0.2M AMMONIUM ACETATE, 30% PEG 4K, SODIUM CITRATE 5.6PH, 10% ISOPROPANOL, 10MM ADP sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.72 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.577 α = 90 b = 88.301 β = 90 c = 116.608 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 CCD ADSC QUANTUM 315 MIRRORS 2009-07-16 M MOLECULAR REPLACEMENT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 50 99.6 0.075 7.3 10 43219 19.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.23 96.4 0.615 5.3 9.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLREP THROUGHOUT PDB ENTRY 3H49 2.15 40.29 40897 40897 1642 94.7 0.226 0.226 0.2167 0.266 0.2579 RANDOM 33.2
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] 5.15 -1.366 -3.784
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.931 c_scbond_it 2.676 c_mcangle_it 2.349 c_mcbond_it 1.475 c_angle_deg 1.4 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.931 c_scbond_it 2.676 c_mcangle_it 2.349 c_mcbond_it 1.475 c_angle_deg 1.4 c_bond_d 0.006 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 c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4736 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 56
Software Software Software Name Purpose CBASS data collection MOLREP phasing CNS refinement DENZO data reduction HKL-2000 data scaling