X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291Protein was concentrated to 16 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: 25% PEG 3350, 0.1 M Bis-tris propane, pH 6.5, 50 mM Na/K phosphate
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.639α = 90
b = 90.828β = 92.832
c = 96.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.96546ESRFMASSIF-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
12.054898.80.1230.1720.1210.9875.9354973
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)
12.052.110.9081.2690.8850.3362.8

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-VALUE7QQI2.054854948271998.6690.1990.19580.254431.144
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]
0.9440.442-0.56-0.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.423
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg7.14
r_lrange_it6.462
r_lrange_other6.45
r_scangle_it4.99
r_scangle_other4.99
r_mcangle_it3.68
r_mcangle_other3.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.423
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg7.14
r_lrange_it6.462
r_lrange_other6.45
r_scangle_it4.99
r_scangle_other4.99
r_mcangle_it3.68
r_mcangle_other3.68
r_scbond_it3.251
r_scbond_other3.25
r_mcbond_other2.591
r_mcbond_it2.59
r_angle_refined_deg1.571
r_angle_other_deg1.28
r_nbd_other0.243
r_symmetry_nbd_refined0.221
r_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.192
r_symmetry_nbd_other0.181
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.171
r_ncsr_local_group_10.106
r_symmetry_nbtor_other0.076
r_chiral_restr0.074
r_symmetry_xyhbond_nbd_other0.074
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7846
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement