6UP5

Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52830.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.1442.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.38α = 90
b = 74.57β = 90
c = 92.87γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2019-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

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
11.9258.1597.60.0560.0680.0380.99512.72.834287
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)
11.921.9797.40.1510.1840.1020.9622.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.9258.1532541170597.150.18390.18130.2322RANDOM24.855
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]
-1.411.240.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.647
r_dihedral_angle_3_deg14.34
r_dihedral_angle_4_deg7.919
r_dihedral_angle_1_deg6.058
r_angle_refined_deg1.367
r_angle_other_deg0.937
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.647
r_dihedral_angle_3_deg14.34
r_dihedral_angle_4_deg7.919
r_dihedral_angle_1_deg6.058
r_angle_refined_deg1.367
r_angle_other_deg0.937
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3719
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing