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Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLM PDB Entry 1RLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 298 PEG 8000, sodium acetate, cacodylic acid, beryllium chloride, magnesium chloride, sodium fluoride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.276 α = 90 b = 91.195 β = 90 c = 176.415 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 2002-06-09 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 4 2002-06-30
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2 2 SYNCHROTRON ALS BEAMLINE 8.3.1 1.000 ALS 8.3.1
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 50 100 0.112 35 5.5 78528 78528 12.5
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 2.03 100 0.108 13.2 3.9 3901
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 Entry 1RLM 2 19.85 77380 77380 7797 98.6 0.235 0.219 0.219 0.2119 0.251 0.2418 RANDOM 25.3
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] -1.77 -1.44 3.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.05 c_mcangle_it 2.1 c_scbond_it 2.08 c_mcbond_it 1.35 c_angle_deg 1.3 c_improper_angle_d 1.26 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8532 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 16
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing