X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.728910 mM BES buffer
Crystal Properties
Matthews coefficientSolvent content
2.4649.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.279α = 90
b = 126.279β = 90
c = 115.361γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

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
11.45115.361000.080.0860.0320.99613.67.3164062
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)
11.451.4799.90.6620.7110.2590.947.5

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 REPLACEMENTTHROUGHOUT1GPB1.4570.71155665829299.950.1320.13010.1698RANDOM26.003
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]
1.631.63-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.533
r_dihedral_angle_4_deg19.165
r_dihedral_angle_3_deg12.011
r_dihedral_angle_1_deg6.3
r_rigid_bond_restr2.764
r_angle_refined_deg1.588
r_angle_other_deg1.515
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.533
r_dihedral_angle_4_deg19.165
r_dihedral_angle_3_deg12.011
r_dihedral_angle_1_deg6.3
r_rigid_bond_restr2.764
r_angle_refined_deg1.588
r_angle_other_deg1.515
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6649
Nucleic Acid Atoms
Solvent Atoms794
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing