X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZV2PDB entry 2ZV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528033% PEG2000 MME, 0.1 M potassium thiocyanate, 0.1 M CHC buffer, pH 7.5, cryoprotectant: 30% polyethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.4950.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.215α = 90
b = 83.174β = 97.27
c = 80.124γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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
12.119.8799.50.10.1240.0730.9969.85.237282
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)
12.12.1699.80.8471.0770.6560.5761.74.7

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 REPLACEMENTTHROUGHOUTPDB entry 2ZV22.119.8735378188599.410.212180.210490.24384RANDOM34.479
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]
-0.78-20.620.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.414
r_dihedral_angle_4_deg18.59
r_dihedral_angle_3_deg12.405
r_dihedral_angle_1_deg5.787
r_long_range_B_refined5.295
r_long_range_B_other5.294
r_mcangle_it3.103
r_mcangle_other3.103
r_scangle_other3.094
r_mcbond_it1.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.414
r_dihedral_angle_4_deg18.59
r_dihedral_angle_3_deg12.405
r_dihedral_angle_1_deg5.787
r_long_range_B_refined5.295
r_long_range_B_other5.294
r_mcangle_it3.103
r_mcangle_other3.103
r_scangle_other3.094
r_mcbond_it1.874
r_mcbond_other1.874
r_scbond_it1.873
r_scbond_other1.861
r_angle_refined_deg1.276
r_angle_other_deg0.896
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms4023
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing