X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2YPDB ENTRY 4V2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.25α = 90
b = 59.656β = 90
c = 86.728γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7537.399.70.0516.984.2330628-3
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)
11.751.8698.70.681.94.23

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 4V2Y1.7537.2929087154099.750.167270.165080.20942RANDOM36.758
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]
1.10.03-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.268
r_dihedral_angle_3_deg13.114
r_dihedral_angle_4_deg12.405
r_dihedral_angle_1_deg6.22
r_mcangle_it2.566
r_scbond_it2.525
r_angle_refined_deg2.235
r_mcbond_it1.665
r_mcbond_other1.664
r_angle_other_deg1.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.268
r_dihedral_angle_3_deg13.114
r_dihedral_angle_4_deg12.405
r_dihedral_angle_1_deg6.22
r_mcangle_it2.566
r_scbond_it2.525
r_angle_refined_deg2.235
r_mcbond_it1.665
r_mcbond_other1.664
r_angle_other_deg1.155
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2232
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling