X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298JBS1D4: 30% PEG 2K MME, 0.1M Na MES pH 6.5, 0.1M Na Acetate
Crystal Properties
Matthews coefficientSolvent content
2.141.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.837α = 90
b = 96.767β = 90
c = 38.372γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0782APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.30948.38498.90.120.1170.1280.0510.99412.211.14825712.29
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3091.33286.80.8210.8060.8870.3250.8968.6

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 REPLACEMENTTHROUGHOUT5C0Z1.3148.3845282235598.80.140.1380.17RANDOM21.32
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]
0.450.69-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.597
r_dihedral_angle_4_deg21.621
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg6.547
r_long_range_B_refined3.301
r_long_range_B_other3.07
r_scangle_other2.988
r_rigid_bond_restr2.664
r_scbond_other2.474
r_scbond_it2.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.597
r_dihedral_angle_4_deg21.621
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg6.547
r_long_range_B_refined3.301
r_long_range_B_other3.07
r_scangle_other2.988
r_rigid_bond_restr2.664
r_scbond_other2.474
r_scbond_it2.471
r_angle_refined_deg2.276
r_mcangle_other1.902
r_mcangle_it1.899
r_mcbond_it1.613
r_mcbond_other1.571
r_angle_other_deg1.236
r_chiral_restr0.155
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.007
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1614
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing