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Deoxyribose-5-phosphate aldolase (DERA) from Geobacillus sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 28% PEG 4000, 0.1 M Tris buffer
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.23 α = 90 b = 57.23 β = 90 c = 97.03 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9688 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.64 34.68 98.4 0.057 0.072 0.043 0.993 10.1 2.56 42879 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.7 98.3 0.684 0.854 0.496 0.503 1.3 2.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1.64 34.67 1.96 42876 1992 98.44 0.1937 0.1916 0.1916 0.2365 0.236 Random selection 31.49
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.6793 f_angle_d 0.8695 f_chiral_restr 0.0554 f_plane_restr 0.0076 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3216 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms
Software Software Software Name Purpose GDA data collection xia2 data reduction DIALS data reduction XDS data reduction XSCALE data scaling Aimless data scaling pointless data scaling PHASER phasing PHENIX refinement