X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292MgCl2, CaCl2, imidazole, MES, MPD, PEG 1000, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9737.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.482α = 90
b = 73.98β = 90
c = 77.715γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.8266PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
10.9553.5899.80.064119.3311.4253359-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.951.0198.81.5920.6051.3910.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3ZR90.9553.58252356101499.780.10470.10460.1199RANDOM13.159
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]
0.71-0.890.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.672
r_sphericity_free20.811
r_dihedral_angle_4_deg18.458
r_dihedral_angle_3_deg11.621
r_sphericity_bonded7.384
r_dihedral_angle_1_deg6.315
r_rigid_bond_restr5.434
r_angle_refined_deg1.428
r_angle_other_deg0.946
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.672
r_sphericity_free20.811
r_dihedral_angle_4_deg18.458
r_dihedral_angle_3_deg11.621
r_sphericity_bonded7.384
r_dihedral_angle_1_deg6.315
r_rigid_bond_restr5.434
r_angle_refined_deg1.428
r_angle_other_deg0.946
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3363
Nucleic Acid Atoms
Solvent Atoms622
Heterogen Atoms30

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing