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Ground state model of human erythroid-specific 5'-aminolevulinate synthase, ALAS2 - SGC Diamond Xchem fragment screening
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HRH 6hrh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.16 α = 90 b = 108 β = 109.21 c = 75.62 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 2M 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.91587 Diamond I02
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 1.95 71.41 98.3 0.074 0.088 0.047 0.998 9.3 3.4 67837
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 1.95 2 97.7 1.072 1.263 0.663 0.621 3.5 4963
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 FOURIER SYNTHESIS THROUGHOUT 6hrh 1.95 71.51 64546 3290 98.11 0.1983 0.1968 0.2059 0.2277 0.2316 RANDOM 36.156
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] 2.34 -0.47 1.63 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.202 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.705 r_mcangle_it 4.064 r_mcbond_other 2.902 r_mcbond_it 2.901 r_angle_refined_deg 1.538 r_angle_other_deg 1.382 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.202 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.705 r_mcangle_it 4.064 r_mcbond_other 2.902 r_mcbond_it 2.901 r_angle_refined_deg 1.538 r_angle_other_deg 1.382 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6605 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing