X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZR1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429328% PEG 10K, 0.1 M Sodium acetate, pH 4.0, 0.2 M Lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.0539.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.26α = 90
b = 71.202β = 90
c = 60.924γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91991BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.947.699.90.210.9957.97.226840
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94100127.1

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 REPLACEMENTTHROUGHOUT3ZR11.947.625407137799.860.186150.183570.23556RANDOM18.274
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]
0.91-0.54-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_4_deg18.846
r_dihedral_angle_3_deg13.372
r_dihedral_angle_1_deg5.981
r_long_range_B_refined5.337
r_long_range_B_other5.337
r_scangle_other2.349
r_mcangle_it1.793
r_mcangle_other1.792
r_scbond_it1.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_4_deg18.846
r_dihedral_angle_3_deg13.372
r_dihedral_angle_1_deg5.981
r_long_range_B_refined5.337
r_long_range_B_other5.337
r_scangle_other2.349
r_mcangle_it1.793
r_mcangle_other1.792
r_scbond_it1.406
r_scbond_other1.406
r_angle_refined_deg1.311
r_mcbond_it1.042
r_mcbond_other1.041
r_angle_other_deg0.914
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2506
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing