X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZQ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529512.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrochloride, and DL-serine; in 0.1 M bicine/Trizma base, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0239.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.462α = 77.26
b = 51.413β = 86.74
c = 77.879γ = 77.63
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-26MSINGLE 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)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
11.445.9393.10.0580.0680.99912.493.58210702821.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4892.70.5820.6790.8282.133.638

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 REPLACEMENTTHROUGHOUT1ZQ51.445.93105499153393.120.1550.15460.1775RANDOM17.31
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]
0.020.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.746
r_dihedral_angle_4_deg18.272
r_dihedral_angle_3_deg12.705
r_dihedral_angle_1_deg6.003
r_angle_other_deg2.252
r_angle_refined_deg1.743
r_chiral_restr0.092
r_bond_other_d0.034
r_gen_planes_other0.015
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.746
r_dihedral_angle_4_deg18.272
r_dihedral_angle_3_deg12.705
r_dihedral_angle_1_deg6.003
r_angle_other_deg2.252
r_angle_refined_deg1.743
r_chiral_restr0.092
r_bond_other_d0.034
r_gen_planes_other0.015
r_bond_refined_d0.011
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5072
Nucleic Acid Atoms
Solvent Atoms728
Heterogen Atoms167

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction