X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XRW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Nacacodylate pH6.0, 15% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4649.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.17α = 90
b = 128.405β = 90
c = 82.905γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.95371CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1219.78699.90.09417.213.528200
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.814

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE219.78628180142199.8410.1950.19260.234538.81
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]
-0.9791.146-0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.941
r_dihedral_angle_4_deg19.549
r_dihedral_angle_3_deg13.029
r_dihedral_angle_1_deg6.353
r_lrange_it5.27
r_lrange_other5.136
r_scangle_it3.195
r_scangle_other3.194
r_mcangle_it2.927
r_mcangle_other2.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.941
r_dihedral_angle_4_deg19.549
r_dihedral_angle_3_deg13.029
r_dihedral_angle_1_deg6.353
r_lrange_it5.27
r_lrange_other5.136
r_scangle_it3.195
r_scangle_other3.194
r_mcangle_it2.927
r_mcangle_other2.926
r_scbond_it1.954
r_scbond_other1.953
r_mcbond_it1.765
r_mcbond_other1.765
r_angle_refined_deg1.162
r_angle_other_deg1.117
r_symmetry_nbd_refined0.195
r_nbd_refined0.192
r_nbd_other0.17
r_symmetry_nbd_other0.158
r_nbtor_refined0.157
r_xyhbond_nbd_refined0.124
r_symmetry_xyhbond_nbd_refined0.107
r_symmetry_nbtor_other0.071
r_chiral_restr0.067
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2763
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing