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Crystal structure of l-fuculose-1-phosphate aldolase from Thermus Thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FK5 PDB ENTRY 2FK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 28% PEG 4000, 0.1M CITRATE-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.405 α = 90 b = 101.403 β = 90 c = 173.223 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 RIGAKU RAXIS IV mirrors 2003-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.6 30 99.5 0.074 46644 45.4
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) 1 2.6 2.69 99.9 0.564
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-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 2FK5 2.7 19.97 40111 2021 95.5 0.225 0.225 0.2234 0.318 0.314 RANDOM 61.5
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] -1.98 -11.71 13.69
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 9.81 c_mcangle_it 7.89 c_scbond_it 7.75 c_mcbond_it 5.52 c_angle_deg 1.5 c_improper_angle_d 1 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 9.81 c_mcangle_it 7.89 c_scbond_it 7.75 c_mcbond_it 5.52 c_angle_deg 1.5 c_improper_angle_d 1 c_bond_d 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11637 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing