X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZBP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M SPG, pH 8, 25 % Peg 1500,
Crystal Properties
Matthews coefficientSolvent content
2.4249.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.42α = 90
b = 108.42β = 90
c = 165.538γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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
12.34941000.05119.910.191842
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.499.60.70.50.87

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-VALUE6ZBP2.3493.89591817464399.9770.1940.19190.227553.178
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]
0.0240.0120.024-0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.378
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg7.729
r_lrange_it5.505
r_lrange_other5.501
r_scangle_it3.385
r_scangle_other3.385
r_mcangle_it3.086
r_mcangle_other3.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.378
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg7.729
r_lrange_it5.505
r_lrange_other5.501
r_scangle_it3.385
r_scangle_other3.385
r_mcangle_it3.086
r_mcangle_other3.086
r_scbond_it2.103
r_scbond_other2.103
r_mcbond_it1.883
r_mcbond_other1.882
r_angle_refined_deg1.611
r_angle_other_deg1.287
r_symmetry_xyhbond_nbd_refined0.275
r_nbd_other0.257
r_symmetry_nbd_refined0.207
r_nbd_refined0.194
r_symmetry_nbd_other0.19
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.137
r_ncsr_local_group_130.091
r_ncsr_local_group_210.091
r_ncsr_local_group_190.089
r_ncsr_local_group_110.088
r_ncsr_local_group_10.087
r_ncsr_local_group_50.087
r_ncsr_local_group_30.085
r_symmetry_nbtor_other0.082
r_ncsr_local_group_250.079
r_ncsr_local_group_40.077
r_ncsr_local_group_290.077
r_ncsr_local_group_140.076
r_ncsr_local_group_200.076
r_ncsr_local_group_120.072
r_ncsr_local_group_20.07
r_chiral_restr0.069
r_ncsr_local_group_170.067
r_ncsr_local_group_220.064
r_ncsr_local_group_280.064
r_ncsr_local_group_160.063
r_ncsr_local_group_80.06
r_ncsr_local_group_270.06
r_ncsr_local_group_300.06
r_ncsr_local_group_260.059
r_ncsr_local_group_230.056
r_ncsr_local_group_150.053
r_ncsr_local_group_90.051
r_ncsr_local_group_60.049
r_ncsr_local_group_100.045
r_ncsr_local_group_180.044
r_ncsr_local_group_240.042
r_ncsr_local_group_70.035
r_symmetry_xyhbond_nbd_other0.016
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15292
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing