X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829320 % w/v Polyethylene glycol 6,000 100 mM Tris pH 8.0 200 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4750.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.037α = 72.6
b = 50.264β = 76.97
c = 76.141γ = 64.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2016-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
1326.7396.70.1735.23.8312288
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)
133.1196.10.4092.13.95

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 REPLACEMENTTHROUGHOUT3UHM326.741165962696.540.270180.26570.35047RANDOM39.701
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]
0.26-0.140.040.130.09-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.907
r_dihedral_angle_4_deg19.804
r_dihedral_angle_3_deg19.37
r_long_range_B_refined6.785
r_long_range_B_other6.783
r_dihedral_angle_1_deg5.861
r_mcangle_it2.789
r_mcangle_other2.788
r_scangle_other2.25
r_mcbond_it1.638
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.907
r_dihedral_angle_4_deg19.804
r_dihedral_angle_3_deg19.37
r_long_range_B_refined6.785
r_long_range_B_other6.783
r_dihedral_angle_1_deg5.861
r_mcangle_it2.789
r_mcangle_other2.788
r_scangle_other2.25
r_mcbond_it1.638
r_mcbond_other1.638
r_angle_refined_deg1.558
r_angle_other_deg1.441
r_scbond_it1.288
r_scbond_other1.288
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
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 Atoms4656
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing