X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZE2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293.1517 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, 20 mM 4-nitrophenol, protein concentration 8 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.3247.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.611α = 90
b = 109.674β = 90
c = 115.634γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.547.2399.50.0860.0960.0420.99710.65.2186872-3.711.1
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)
11.51.5399.20.9081.0080.4290.6681.75.3

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6ZE21.547.23186795945599.3410.1560.1560.154870.18162random selection15.971
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]
0.31-0.7390.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.14
r_dihedral_angle_4_deg18.524
r_dihedral_angle_3_deg12.296
r_dihedral_angle_1_deg7.064
r_lrange_it4.508
r_lrange_other4.177
r_scangle_it2.846
r_scangle_other2.845
r_scbond_it1.922
r_scbond_other1.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.14
r_dihedral_angle_4_deg18.524
r_dihedral_angle_3_deg12.296
r_dihedral_angle_1_deg7.064
r_lrange_it4.508
r_lrange_other4.177
r_scangle_it2.846
r_scangle_other2.845
r_scbond_it1.922
r_scbond_other1.922
r_mcangle_it1.894
r_mcangle_other1.894
r_angle_refined_deg1.776
r_angle_other_deg1.478
r_mcbond_it1.349
r_mcbond_other1.348
r_nbd_refined0.209
r_symmetry_nbd_other0.187
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.164
r_nbd_other0.156
r_xyhbond_nbd_refined0.152
r_symmetry_xyhbond_nbd_refined0.146
r_metal_ion_refined0.097
r_chiral_restr0.095
r_symmetry_nbd_refined0.092
r_symmetry_nbtor_other0.084
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8923
Nucleic Acid Atoms
Solvent Atoms1489
Heterogen Atoms360

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing