X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293PEG 3350, DL-malic acid
Crystal Properties
Matthews coefficientSolvent content
2.4249.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.643α = 90
b = 49.464β = 91.21
c = 119.494γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2021-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0SPring-8BL32XU

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
11.945099.30.320.3510.2050.9295.613.1683643
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)
11.942.0598.91.4051.5560.9290.5231.072.99

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 REPLACEMENTTHROUGHOUT5HXT1.9449.3640769226099.910.202980.199990.25502RANDOM48.375
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]
-2.311.244.42-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_3_deg17.049
r_dihedral_angle_4_deg14.345
r_long_range_B_refined9.711
r_long_range_B_other9.692
r_scangle_other7.242
r_dihedral_angle_1_deg6.654
r_mcangle_it5.347
r_mcangle_other5.347
r_scbond_it4.731
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_3_deg17.049
r_dihedral_angle_4_deg14.345
r_long_range_B_refined9.711
r_long_range_B_other9.692
r_scangle_other7.242
r_dihedral_angle_1_deg6.654
r_mcangle_it5.347
r_mcangle_other5.347
r_scbond_it4.731
r_scbond_other4.729
r_mcbond_it3.695
r_mcbond_other3.694
r_angle_refined_deg1.509
r_angle_other_deg1.273
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3819
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing