X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.62α = 90
b = 34.62β = 90
c = 99.48γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
11.682096.80.05317.6572617261-3-326
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7599.60.4223.74.9824

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6820-37259725936396.890.191560.191560.189970.22235RANDOM22.21
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]
1.011.01-2.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg27.177
r_dihedral_angle_2_deg20.227
r_dihedral_angle_3_deg9.87
r_dihedral_angle_1_deg5.376
r_scangle_it2.022
r_scbond_it1.573
r_mcangle_it1.163
r_angle_refined_deg1.162
r_mcbond_it0.987
r_angle_other_deg0.731
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg27.177
r_dihedral_angle_2_deg20.227
r_dihedral_angle_3_deg9.87
r_dihedral_angle_1_deg5.376
r_scangle_it2.022
r_scbond_it1.573
r_mcangle_it1.163
r_angle_refined_deg1.162
r_mcbond_it0.987
r_angle_other_deg0.731
r_symmetry_vdw_refined0.243
r_nbd_other0.241
r_symmetry_vdw_other0.209
r_nbd_refined0.189
r_mcbond_other0.176
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.132
r_nbtor_other0.083
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms450
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing