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PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z1171217421
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 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.26 α = 90 b = 108.655 β = 109.31 c = 75.747 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 6M 2019-02-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.46 71.49 99.1 0.041 0.05 0.027 0.999 10.5 3 164159
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 1.46 1.54 97.8 1.212 1.561 0.972 0.447 2.1 23607
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 1.46 71.59 155310 8032 98.49 0.213 0.212 0.2195 0.2317 0.2395 RANDOM 25.459
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] 1.67 -0.02 0.28 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.187 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 14.725 r_dihedral_angle_1_deg 6.768 r_mcangle_it 2.793 r_mcbond_it 2.022 r_mcbond_other 2.021 r_angle_refined_deg 1.684 r_angle_other_deg 1.485 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.187 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 14.725 r_dihedral_angle_1_deg 6.768 r_mcangle_it 2.793 r_mcbond_it 2.022 r_mcbond_other 2.021 r_angle_refined_deg 1.684 r_angle_other_deg 1.485 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6617 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing