X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6S9V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
1.9537

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.798α = 90
b = 94.409β = 90
c = 104.772γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2020-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.364699.70.0760.0950.0560.99910.7595834
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.381.271.5830.9330.455

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-VALUE6S9V1.364695748484499.5640.1510.14950.185316.554
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]
-0.567-1.9152.483
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.472
r_dihedral_angle_4_deg14.923
r_dihedral_angle_3_deg11.739
r_rigid_bond_restr7.317
r_dihedral_angle_1_deg6.556
r_lrange_it3.062
r_lrange_other2.805
r_scangle_it2.46
r_scangle_other2.46
r_scbond_it2.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.472
r_dihedral_angle_4_deg14.923
r_dihedral_angle_3_deg11.739
r_rigid_bond_restr7.317
r_dihedral_angle_1_deg6.556
r_lrange_it3.062
r_lrange_other2.805
r_scangle_it2.46
r_scangle_other2.46
r_scbond_it2.036
r_scbond_other2.035
r_mcangle_other1.714
r_mcangle_it1.711
r_angle_other_deg1.421
r_mcbond_it1.372
r_angle_refined_deg1.364
r_mcbond_other1.357
r_nbd_refined0.21
r_symmetry_nbd_other0.182
r_nbtor_refined0.173
r_symmetry_nbd_refined0.173
r_nbd_other0.17
r_symmetry_xyhbond_nbd_refined0.161
r_xyhbond_nbd_refined0.136
r_symmetry_xyhbond_nbd_other0.079
r_symmetry_nbtor_other0.077
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3918
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement