X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES293Sodium Malonate
Crystal Properties
Matthews coefficientSolvent content
1.8834.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.9α = 90
b = 66.9β = 90
c = 40.8γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300PIXELAGIPD2019-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASEREUROPEAN XFEL BEAMLINE SPB/SFX1.33European XFELSPB/SFX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.611.8193.2713.98287.612318
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.641

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.611.811231862093.270.222750.220570.26651RANDOM7.007
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]
0.010.010.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.157
r_dihedral_angle_3_deg18.429
r_dihedral_angle_4_deg17.303
r_dihedral_angle_1_deg8.987
r_angle_refined_deg2.543
r_long_range_B_refined1.853
r_long_range_B_other1.559
r_angle_other_deg1.115
r_mcangle_it0.683
r_mcangle_other0.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.157
r_dihedral_angle_3_deg18.429
r_dihedral_angle_4_deg17.303
r_dihedral_angle_1_deg8.987
r_angle_refined_deg2.543
r_long_range_B_refined1.853
r_long_range_B_other1.559
r_angle_other_deg1.115
r_mcangle_it0.683
r_mcangle_other0.683
r_scangle_other0.502
r_mcbond_it0.457
r_mcbond_other0.457
r_scbond_it0.326
r_scbond_other0.326
r_chiral_restr0.153
r_bond_refined_d0.025
r_gen_planes_refined0.013
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 Atoms987
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing