X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XA7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6291Sodium Cacodylate 0.085M pH 6.0 + PEG 8K 21% + Glycerol 15%
Crystal Properties
Matthews coefficientSolvent content
2.3848.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.027α = 90
b = 107.943β = 109.454
c = 56.39γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1247.799.90.050.0220.99915.46.235815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051001.7580.7670.5891.16.2

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-VALUE247.69835785179799.8910.190.18760.232358.404
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]
-0.0090.008-0.0110.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.345
r_dihedral_angle_3_deg16.034
r_dihedral_angle_2_deg10.611
r_lrange_it9.394
r_lrange_other9.393
r_scangle_other7.142
r_scangle_it6.985
r_dihedral_angle_1_deg6.573
r_mcangle_it5.901
r_mcangle_other5.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.345
r_dihedral_angle_3_deg16.034
r_dihedral_angle_2_deg10.611
r_lrange_it9.394
r_lrange_other9.393
r_scangle_other7.142
r_scangle_it6.985
r_dihedral_angle_1_deg6.573
r_mcangle_it5.901
r_mcangle_other5.9
r_scbond_it4.746
r_scbond_other4.745
r_mcbond_it4.292
r_mcbond_other4.283
r_angle_refined_deg1.288
r_angle_other_deg0.467
r_nbd_refined0.207
r_symmetry_nbd_other0.195
r_nbd_other0.193
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.176
r_symmetry_nbd_refined0.127
r_symmetry_xyhbond_nbd_refined0.09
r_symmetry_nbtor_other0.077
r_ncsr_local_group_10.074
r_chiral_restr0.061
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4156
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing