X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DSM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.9358.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.723α = 90
b = 58.709β = 104.132
c = 101.894γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.89843DiamondI03

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
12.370.281000.2310.2730.1440.9845.16.841492
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)
12.32.380.9571.1420.6170.6966.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE3DSM2.370.27641442200199.9060.2250.22280.26833.532
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]
1.8122.426-3.160.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.639
r_dihedral_angle_3_deg14.595
r_dihedral_angle_2_deg8.848
r_dihedral_angle_1_deg8.379
r_lrange_it4.915
r_lrange_other4.915
r_dihedral_angle_other_2_deg4.236
r_scangle_it3.459
r_scangle_other3.459
r_mcangle_other2.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.639
r_dihedral_angle_3_deg14.595
r_dihedral_angle_2_deg8.848
r_dihedral_angle_1_deg8.379
r_lrange_it4.915
r_lrange_other4.915
r_dihedral_angle_other_2_deg4.236
r_scangle_it3.459
r_scangle_other3.459
r_mcangle_other2.968
r_mcangle_it2.961
r_scbond_it2.312
r_scbond_other2.312
r_mcbond_it1.961
r_mcbond_other1.92
r_angle_refined_deg1.79
r_angle_other_deg0.669
r_symmetry_nbd_other0.199
r_nbd_refined0.187
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.171
r_nbd_other0.154
r_symmetry_nbd_refined0.094
r_symmetry_nbtor_other0.087
r_chiral_restr0.075
r_symmetry_xyhbond_nbd_refined0.066
r_ncsr_local_group_10.059
r_symmetry_xyhbond_nbd_other0.026
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5440
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms246

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing