9DZ7 | pdb_00009dz7

Structure of ALAS bound to glycine 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, 25% v/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.672α = 115.76
b = 112.518β = 98.31
c = 117.388γ = 91.49
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
12.48748.91298.40.1770.9886.273.69370343.52
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)
12.492.6397.90.8920.5771.433.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.48748.9188660504498.590.16980.167610.17630.20740.2124RANDOM48.209
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]
-0.48-0.51-0.65-0.23-0.390.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.672
r_dihedral_angle_3_deg15.699
r_dihedral_angle_1_deg6.208
r_long_range_B_other5.523
r_long_range_B_refined5.522
r_scangle_other3.607
r_mcangle_it2.82
r_mcangle_other2.82
r_scbond_it2.349
r_scbond_other2.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.672
r_dihedral_angle_3_deg15.699
r_dihedral_angle_1_deg6.208
r_long_range_B_other5.523
r_long_range_B_refined5.522
r_scangle_other3.607
r_mcangle_it2.82
r_mcangle_other2.82
r_scbond_it2.349
r_scbond_other2.349
r_mcbond_it1.807
r_mcbond_other1.807
r_angle_refined_deg1.286
r_angle_other_deg0.447
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21950
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms161

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing