5QRE

PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z117233350


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
2.3447.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.849α = 90
b = 108.49β = 109.14
c = 75.748γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-05SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.67671.5694.70.1170.0630.9978.53.468247
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)RedundancyNumber Unique Reflections (All)
11.6761.87574.60.8350.4490.6643.43412

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 SYNTHESISTHROUGHOUT6hrh1.6771.6664932331861.060.21320.21190.2403RANDOM21.51
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]
0.34-0.01-0.11-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.963
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg15.961
r_dihedral_angle_1_deg6.561
r_mcangle_it2.503
r_mcbond_it1.59
r_mcbond_other1.589
r_angle_refined_deg1.482
r_angle_other_deg1.34
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.963
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg15.961
r_dihedral_angle_1_deg6.561
r_mcangle_it2.503
r_mcbond_it1.59
r_mcbond_other1.589
r_angle_refined_deg1.482
r_angle_other_deg1.34
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing