5QT3

Ground state model of human erythroid-specific 5'-aminolevulinate synthase, ALAS2 - SGC Diamond Xchem fragment screening


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3146.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.16α = 90
b = 108β = 109.21
c = 75.62γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2019-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.91587DiamondI02

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9571.4198.30.0740.0880.0470.9989.33.467837
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)RedundancyNumber Unique Reflections (All)
11.95297.71.0721.2630.6630.6213.54963

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6hrh1.9571.5164546329098.110.19830.19680.2277RANDOM36.156
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]
2.34-0.471.63-2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.202
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg6.705
r_mcangle_it4.064
r_mcbond_other2.902
r_mcbond_it2.901
r_angle_refined_deg1.538
r_angle_other_deg1.382
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.202
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg6.705
r_mcangle_it4.064
r_mcbond_other2.902
r_mcbond_it2.901
r_angle_refined_deg1.538
r_angle_other_deg1.382
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6605
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing