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Transition State Analogue of ybiV from E. coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLM PDB ID 1RLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 298 PEG 8000, sodium acetate, aluminum chloride, sodium fluoride, cacodylic acid, magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.761 α = 90 b = 91.166 β = 90 c = 183.85 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 4 2002-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 2.2 50 99.7 0.08 31 5.4 61606 61606 20.9
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 2.2 2.24 100 0.25 5 5 3058
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 (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ID 1RLM 2.2 19.93 59839 59839 6051 96.5 0.242 0.221 0.221 0.2088 0.264 0.2495 RANDOM 40.9
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] -10.02 -6.63 16.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 5.32 c_mcangle_it 3.55 c_scbond_it 3.42 c_mcbond_it 2.07 c_angle_deg 1.8 c_improper_angle_d 1.22 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8516 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 36
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing