X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MBG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400
Crystal Properties
Matthews coefficientSolvent content
2.6152.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.686α = 90
b = 102.808β = 91.289
c = 101.554γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRIUS BEAMLINE MANACA0.977180LNLS SIRIUSMANACA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.66101.5346.10.9683.73.274929
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.720.463

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7mbg1.664101.52874928369046.1080.210.20770.250619.413
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]
-1.973-0.318-3.4085.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.36
r_dihedral_angle_4_deg18.383
r_dihedral_angle_3_deg16.949
r_dihedral_angle_1_deg8.792
r_lrange_it6.285
r_lrange_other6.061
r_mcangle_it2.264
r_mcangle_other2.264
r_scangle_it2.225
r_scangle_other2.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.36
r_dihedral_angle_4_deg18.383
r_dihedral_angle_3_deg16.949
r_dihedral_angle_1_deg8.792
r_lrange_it6.285
r_lrange_other6.061
r_mcangle_it2.264
r_mcangle_other2.264
r_scangle_it2.225
r_scangle_other2.225
r_angle_refined_deg1.973
r_mcbond_it1.484
r_mcbond_other1.484
r_scbond_it1.475
r_scbond_other1.475
r_angle_other_deg1.254
r_xyhbond_nbd_refined0.415
r_symmetry_xyhbond_nbd_refined0.395
r_symmetry_nbd_refined0.265
r_nbd_other0.235
r_nbd_refined0.218
r_symmetry_nbd_other0.208
r_symmetry_xyhbond_nbd_other0.191
r_nbtor_refined0.165
r_xyhbond_nbd_other0.149
r_chiral_restr0.091
r_symmetry_nbtor_other0.083
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9356
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing