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PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z2856434899
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 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.696 α = 90 b = 108.463 β = 108.98 c = 75.697 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 2019-04-05 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) 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 1.493 55.437 93.3 0.059 0.032 0.999 12.6 3.4 100570
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.493 1.655 79.6 0.691 0.412 0.669 2.7 5031
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 1.49 71.69 95630 4941 64.79 0.2102 0.2091 0.2168 0.2323 0.2381 RANDOM 19.54
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] 0.11 0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.364 r_dihedral_angle_4_deg 18.37 r_dihedral_angle_3_deg 14.927 r_dihedral_angle_1_deg 6.669 r_mcangle_it 2.419 r_angle_refined_deg 1.628 r_mcbond_it 1.618 r_mcbond_other 1.616 r_angle_other_deg 1.429 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.364 r_dihedral_angle_4_deg 18.37 r_dihedral_angle_3_deg 14.927 r_dihedral_angle_1_deg 6.669 r_mcangle_it 2.419 r_angle_refined_deg 1.628 r_mcbond_it 1.618 r_mcbond_other 1.616 r_angle_other_deg 1.429 r_chiral_restr 0.083 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 250 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing