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, Na cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.775α = 90
b = 66.988β = 90
c = 67.759γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2021-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7633.997.880.99927.64.727041
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.8060.784

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IXF1.7633.927041125597.8820.1960.19460.232335.759
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]
1.776-0.601-1.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.278
r_dihedral_angle_4_deg20.945
r_dihedral_angle_3_deg18.077
r_lrange_it7.705
r_lrange_other7.701
r_dihedral_angle_1_deg5.844
r_scangle_it4.034
r_scangle_other4.025
r_mcangle_other2.913
r_mcangle_it2.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.278
r_dihedral_angle_4_deg20.945
r_dihedral_angle_3_deg18.077
r_lrange_it7.705
r_lrange_other7.701
r_dihedral_angle_1_deg5.844
r_scangle_it4.034
r_scangle_other4.025
r_mcangle_other2.913
r_mcangle_it2.912
r_scbond_it2.731
r_scbond_other2.719
r_mcbond_it2.057
r_mcbond_other2.056
r_angle_refined_deg1.848
r_angle_other_deg1.547
r_nbd_refined0.271
r_symmetry_nbd_other0.211
r_nbtor_refined0.185
r_nbd_other0.172
r_xyhbond_nbd_refined0.156
r_symmetry_xyhbond_nbd_refined0.104
r_chiral_restr0.094
r_symmetry_nbtor_other0.087
r_symmetry_nbd_refined0.075
r_chiral_restr_other0.045
r_symmetry_xyhbond_nbd_other0.041
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2129
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms134

Software

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