9DZO | pdb_00009dzo

Structure of ALAS bound to succinyl-CoA from S. cerevisiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TXR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.15 M magnesium chloride, 0.1 M HEPES, pH 7.5, 22.5% v/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2645.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.595α = 116.403
b = 114.241β = 97.507
c = 119.307γ = 91.839
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.920105NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.6948.7798.50.2350.9785.33.67742537.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.692.84981.1510.5071.223.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.69148.76977425384798.6730.1820.18010.1860.22670.231RANDOM50.143
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]
0.965-0.043-0.1330.669-0.007-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.281
r_dihedral_angle_6_deg13.87
r_dihedral_angle_2_deg12.339
r_lrange_it5.994
r_lrange_other5.98
r_dihedral_angle_1_deg5.896
r_scangle_it4.512
r_scangle_other4.512
r_scbond_it2.897
r_scbond_other2.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.281
r_dihedral_angle_6_deg13.87
r_dihedral_angle_2_deg12.339
r_lrange_it5.994
r_lrange_other5.98
r_dihedral_angle_1_deg5.896
r_scangle_it4.512
r_scangle_other4.512
r_scbond_it2.897
r_scbond_other2.881
r_mcangle_it2.82
r_mcangle_other2.82
r_mcbond_it1.761
r_mcbond_other1.76
r_angle_refined_deg1.393
r_angle_other_deg0.489
r_dihedral_angle_other_2_deg0.301
r_nbd_other0.271
r_symmetry_nbd_refined0.209
r_nbd_refined0.204
r_symmetry_nbd_other0.192
r_xyhbond_nbd_refined0.178
r_nbtor_refined0.173
r_symmetry_nbtor_other0.077
r_ncsr_local_group_10.072
r_ncsr_local_group_30.069
r_ncsr_local_group_40.069
r_ncsr_local_group_60.068
r_ncsr_local_group_100.067
r_ncsr_local_group_20.066
r_symmetry_xyhbond_nbd_refined0.065
r_chiral_restr0.064
r_ncsr_local_group_50.064
r_ncsr_local_group_70.064
r_ncsr_local_group_80.064
r_ncsr_local_group_90.064
r_ncsr_local_group_120.062
r_ncsr_local_group_130.062
r_ncsr_local_group_140.062
r_ncsr_local_group_110.059
r_ncsr_local_group_150.059
r_symmetry_xyhbond_nbd_other0.04
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22230
Nucleic Acid Atoms
Solvent Atoms629
Heterogen Atoms356

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing