X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EM0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72772.8M sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
2.5451.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.608α = 90
b = 59.237β = 90.02
c = 82.911γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2018-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97933APS19-BM

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)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
12.44099.20.0370.0370.0420.02631.82.519535-3
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)
12.42.441000.3090.3090.6070.3680.8762.32.5

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 REPLACEMENTTHROUGHOUT5em02.432.261852499099.160.232560.230930.2611RANDOM94.246
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]
-4.991.721.13.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.775
r_dihedral_angle_4_deg29.421
r_dihedral_angle_3_deg13.667
r_dihedral_angle_1_deg8.132
r_long_range_B_refined4.219
r_long_range_B_other4.21
r_mcangle_it1.493
r_mcangle_other1.493
r_scangle_other1.389
r_angle_refined_deg1.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.775
r_dihedral_angle_4_deg29.421
r_dihedral_angle_3_deg13.667
r_dihedral_angle_1_deg8.132
r_long_range_B_refined4.219
r_long_range_B_other4.21
r_mcangle_it1.493
r_mcangle_other1.493
r_scangle_other1.389
r_angle_refined_deg1.294
r_mcbond_it0.878
r_mcbond_other0.877
r_scbond_it0.854
r_scbond_other0.853
r_angle_other_deg0.836
r_chiral_restr0.063
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2889
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
BUCCANEERmodel building
HKL-2000data processing