X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729320 % w/v Polyethylene glycol 6,000 100 mM HEPES pH 7.0 200 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4349.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.367α = 90
b = 51.18β = 108.22
c = 96.763γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2016-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54184

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
1223.3196.90.07713.77.4741967
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)
122.0794.40.3135.67.32

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 REPLACEMENTTHROUGHOUT3UHM223.3239816215096.830.18960.186850.24088RANDOM32.92
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]
-0.02-0.020.07-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.738
r_dihedral_angle_4_deg16.759
r_dihedral_angle_3_deg16.141
r_dihedral_angle_1_deg7.742
r_long_range_B_refined7.486
r_long_range_B_other7.471
r_scangle_other5.656
r_mcangle_it4.083
r_mcangle_other4.082
r_scbond_it3.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.738
r_dihedral_angle_4_deg16.759
r_dihedral_angle_3_deg16.141
r_dihedral_angle_1_deg7.742
r_long_range_B_refined7.486
r_long_range_B_other7.471
r_scangle_other5.656
r_mcangle_it4.083
r_mcangle_other4.082
r_scbond_it3.619
r_scbond_other3.614
r_mcbond_it2.773
r_mcbond_other2.77
r_angle_refined_deg1.601
r_angle_other_deg1.323
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4642
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing