X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BMX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Optimised from Index H8, 0.1MgFormate 15% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8456.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.77α = 90
b = 131.04β = 90
c = 179.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9794DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.674.799.40.060.9911.813.254678
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.680.661.1

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-VALUE2.674.12354607267599.2530.2210.21820.27671.314
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]
-3.3164.184-0.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.463
r_dihedral_angle_6_deg15.96
r_dihedral_angle_2_deg13.158
r_lrange_it10.071
r_lrange_other10.071
r_dihedral_angle_1_deg9.311
r_scangle_it8.54
r_scangle_other8.539
r_mcangle_it7.744
r_mcangle_other7.744
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.463
r_dihedral_angle_6_deg15.96
r_dihedral_angle_2_deg13.158
r_lrange_it10.071
r_lrange_other10.071
r_dihedral_angle_1_deg9.311
r_scangle_it8.54
r_scangle_other8.539
r_mcangle_it7.744
r_mcangle_other7.744
r_scbond_it5.969
r_scbond_other5.969
r_mcbond_it5.535
r_mcbond_other5.534
r_angle_refined_deg2.466
r_angle_other_deg0.896
r_xyhbond_nbd_refined0.192
r_symmetry_nbd_refined0.183
r_nbd_other0.177
r_nbd_refined0.174
r_nbtor_refined0.17
r_symmetry_nbd_other0.166
r_symmetry_xyhbond_nbd_refined0.154
r_chiral_restr0.132
r_ncsr_local_group_30.117
r_ncsr_local_group_20.116
r_ncsr_local_group_10.111
r_ncsr_local_group_60.108
r_ncsr_local_group_40.106
r_ncsr_local_group_50.094
r_symmetry_nbtor_other0.081
r_bond_refined_d0.014
r_symmetry_xyhbond_nbd_other0.014
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10619
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms372

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing