6SBJ

X-ray structure of mus musculus Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) apo-form uuncomplexed


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FOH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529325% (w/v) PEG 3350, 0.2 M MgCl2 and 0.1 M Bis/Tris pH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.6827

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.401α = 90
b = 69.959β = 92.25
c = 107.557γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

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
12.21742.6589.20.2510.2980.1590.9634.63.442614422.6
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)
12.2172.46645.60.9581.1380.6090.5531.43.38

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6FOH2.2242.6524929121967.320.19620.19330.2574RANDOM27.656
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]
0.090.56-0.02-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.696
r_dihedral_angle_3_deg19.104
r_dihedral_angle_4_deg16.639
r_dihedral_angle_1_deg8.129
r_angle_refined_deg1.601
r_angle_other_deg1.222
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.696
r_dihedral_angle_3_deg19.104
r_dihedral_angle_4_deg16.639
r_dihedral_angle_1_deg8.129
r_angle_refined_deg1.601
r_angle_other_deg1.222
r_chiral_restr0.066
r_bond_refined_d0.01
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 Atoms6449
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing