X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UPM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.5298100 mM ammonium acetate, 100 mM bis-Tris, and 17% w/v polyethylene glycol 3350.
Crystal Properties
Matthews coefficientSolvent content
2.0840.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.31α = 90
b = 67.76β = 90
c = 83.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2017-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.245.3196.30.170.986.94.712754
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.382.40.8370.5251.94.5

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 REPLACEMENTTHROUGHOUT5UPM2.245.311275469597.90.218370.216050.26042RANDOM22.694
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]
1.26-0.39-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.076
r_dihedral_angle_3_deg14.785
r_dihedral_angle_4_deg12.02
r_dihedral_angle_1_deg6.487
r_long_range_B_refined4.494
r_long_range_B_other4.494
r_scangle_other2.627
r_mcangle_it2.143
r_mcangle_other2.142
r_angle_refined_deg1.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.076
r_dihedral_angle_3_deg14.785
r_dihedral_angle_4_deg12.02
r_dihedral_angle_1_deg6.487
r_long_range_B_refined4.494
r_long_range_B_other4.494
r_scangle_other2.627
r_mcangle_it2.143
r_mcangle_other2.142
r_angle_refined_deg1.937
r_scbond_it1.569
r_scbond_other1.569
r_mcbond_it1.271
r_mcbond_other1.27
r_angle_other_deg1.024
r_chiral_restr0.344
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms1856
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction