X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MI4PDB entry 4MI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52910.01 M magnesium chloride, 0.1 M Tris, 2% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.5451.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.979α = 90
b = 186.502β = 90
c = 73.722γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300beryllium lenses2015-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.3530990.05333.957.5276661
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)
11.351.3797.80.6533.137.4

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 4MI41.35302627231391498.80.124730.123340.1512RANDOM18.579
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]
-0.28-0.360.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.426
r_dihedral_angle_4_deg17.267
r_sphericity_free15.808
r_dihedral_angle_3_deg11.741
r_sphericity_bonded8.672
r_dihedral_angle_1_deg5.956
r_long_range_B_refined3.489
r_rigid_bond_restr3.147
r_long_range_B_other2.685
r_scangle_other2.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.426
r_dihedral_angle_4_deg17.267
r_sphericity_free15.808
r_dihedral_angle_3_deg11.741
r_sphericity_bonded8.672
r_dihedral_angle_1_deg5.956
r_long_range_B_refined3.489
r_rigid_bond_restr3.147
r_long_range_B_other2.685
r_scangle_other2.622
r_scbond_it2.165
r_scbond_other2.164
r_mcangle_other1.75
r_mcangle_it1.746
r_angle_refined_deg1.721
r_mcbond_it1.403
r_mcbond_other1.394
r_angle_other_deg1.039
r_chiral_restr0.118
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8681
Nucleic Acid Atoms
Solvent Atoms1471
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building