X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277MPEG 2000, ammonium sulfate, sodium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.043α = 90
b = 67.614β = 90
c = 67.566γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2019-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.744.4799.520.0510.0230.99731.54.728874218.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.74394.90.5440.2640.7753.9

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 REPLACEMENTTHROUGHOUT3IXF1.744.4728874144899.520.165890.163860.20598RANDOM18.911
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]
4.79-3.55-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.409
r_dihedral_angle_4_deg21.807
r_dihedral_angle_3_deg18.308
r_dihedral_angle_1_deg5.522
r_long_range_B_refined4.93
r_long_range_B_other4.753
r_scangle_other3.144
r_mcangle_it2.307
r_mcangle_other2.307
r_scbond_it2.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.409
r_dihedral_angle_4_deg21.807
r_dihedral_angle_3_deg18.308
r_dihedral_angle_1_deg5.522
r_long_range_B_refined4.93
r_long_range_B_other4.753
r_scangle_other3.144
r_mcangle_it2.307
r_mcangle_other2.307
r_scbond_it2.157
r_scbond_other2.136
r_angle_refined_deg1.837
r_mcbond_it1.644
r_mcbond_other1.64
r_angle_other_deg1.483
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.001
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 Atoms2162
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms157

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing