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Crystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model built based on an experimental map
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 2M Ammonium sulfate, 0.15M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.288 α = 90 b = 57.309 β = 90 c = 94.2 γ = 90
Symmetry Space Group P 21 21 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 CCD MARRESEARCH Diamond monochromator and downstream mirror 2004-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.98 APS 31-ID
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 2.8 20 93.1 0.08 11.04 38306 38306 -3 59.5
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) 1 2.8 2.9 92.9 0.382 2.05 3849
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD aided by MR THROUGHOUT 2.8 19.72 35774 1813 86.7 0.2151 0.215 0.2338 0.247 0.2598 RANDOM 41.5
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] -9.57 17.74 -8.18
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.27 c_scbond_it 2.33 c_mcangle_it 1.89 c_mcbond_it 1.11 c_angle_deg 1.1 c_improper_angle_d 0.68 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5352 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 45
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing CNS refinement