X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol
Crystal Properties
Matthews coefficientSolvent content
238.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.76α = 90
b = 53.98β = 101.18
c = 114.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978564SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.74348.64950.9937.726.252176
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)
11.7431.8569.20.509

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-VALUE7K3T1.74343.94952172260995.010.210.20730.254729.063
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]
0.126-1.2210.3110.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.565
r_dihedral_angle_4_deg20.42
r_dihedral_angle_3_deg14.528
r_dihedral_angle_1_deg7.834
r_lrange_other6.356
r_lrange_it6.354
r_scangle_it4.362
r_scangle_other4.362
r_mcangle_it3.406
r_mcangle_other3.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.565
r_dihedral_angle_4_deg20.42
r_dihedral_angle_3_deg14.528
r_dihedral_angle_1_deg7.834
r_lrange_other6.356
r_lrange_it6.354
r_scangle_it4.362
r_scangle_other4.362
r_mcangle_it3.406
r_mcangle_other3.406
r_scbond_it2.782
r_scbond_other2.781
r_mcbond_it2.277
r_mcbond_other2.277
r_angle_refined_deg1.538
r_angle_other_deg1.353
r_symmetry_xyhbond_nbd_refined0.207
r_nbd_refined0.195
r_xyhbond_nbd_refined0.188
r_symmetry_nbd_other0.179
r_xyhbond_nbd_other0.179
r_symmetry_nbd_refined0.173
r_nbd_other0.172
r_nbtor_refined0.167
r_symmetry_nbtor_other0.074
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4727
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing
XDSdata processing
Cootmodel building