X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FB9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52910.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, protein concentration 10 mg/ml
Crystal Properties
Matthews coefficientSolvent content
1.9938.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.04α = 107.184
b = 48.186β = 90.114
c = 65.232γ = 105.618
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0332PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.0644.286.020.0850.99783.6187610-3.79.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.061.08864.471.1450.3731.23.4

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5FB91.0644.2187610942386.0150.120.12050.11810.1468Random13.44
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]
-0.498-0.01-0.0110.2720.0950.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.339
r_dihedral_angle_3_deg11.128
r_dihedral_angle_4_deg9.861
r_dihedral_angle_1_deg6.17
r_dihedral_angle_other_3_deg4.494
r_rigid_bond_restr2.495
r_scangle_it1.914
r_scangle_other1.914
r_angle_other_deg1.716
r_scbond_it1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.339
r_dihedral_angle_3_deg11.128
r_dihedral_angle_4_deg9.861
r_dihedral_angle_1_deg6.17
r_dihedral_angle_other_3_deg4.494
r_rigid_bond_restr2.495
r_scangle_it1.914
r_scangle_other1.914
r_angle_other_deg1.716
r_scbond_it1.67
r_angle_refined_deg1.658
r_mcangle_other1.308
r_mcangle_it1.295
r_mcbond_it1.047
r_mcbond_other1.031
r_symmetry_nbd_refined0.243
r_nbd_refined0.233
r_nbd_other0.207
r_nbtor_refined0.183
r_symmetry_nbd_other0.172
r_symmetry_xyhbond_nbd_refined0.142
r_xyhbond_nbd_refined0.14
r_chiral_restr0.104
r_metal_ion_refined0.091
r_symmetry_nbtor_other0.088
r_bond_refined_d0.011
r_bond_other_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4075
Nucleic Acid Atoms
Solvent Atoms770
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building