X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CJRPDB entry 2CJR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529220.0 mg/mL protein in 0.1 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II screen D8 (0.1 M HEPES, pH 7.5, 25% w/v PEG3350)
Crystal Properties
Matthews coefficientSolvent content
2.1542.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.612α = 90
b = 122.317β = 90
c = 130.633γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe2020-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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)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
12.0530970.1710.1710.1870.0730.9769.76.243336-317.1
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)
12.052.0980.60.630.630.6970.2880.6982.65.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 2CJR2.05229.88143303219296.8570.1890.18690.227518.645
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]
1.169-0.386-0.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.429
r_dihedral_angle_4_deg9.126
r_dihedral_angle_3_deg7.608
r_lrange_it4.641
r_lrange_other4.398
r_dihedral_angle_1_deg2.439
r_scangle_it1.621
r_scangle_other1.621
r_angle_refined_deg1.493
r_mcangle_it1.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.429
r_dihedral_angle_4_deg9.126
r_dihedral_angle_3_deg7.608
r_lrange_it4.641
r_lrange_other4.398
r_dihedral_angle_1_deg2.439
r_scangle_it1.621
r_scangle_other1.621
r_angle_refined_deg1.493
r_mcangle_it1.322
r_mcangle_other1.322
r_scbond_it0.96
r_scbond_other0.96
r_mcbond_it0.769
r_mcbond_other0.769
r_angle_other_deg0.394
r_nbd_refined0.208
r_nbd_other0.191
r_symmetry_nbd_refined0.187
r_symmetry_nbd_other0.179
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.132
r_symmetry_xyhbond_nbd_refined0.115
r_symmetry_nbtor_other0.095
r_chiral_restr0.072
r_gen_planes_refined0.053
r_gen_planes_other0.048
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5196
Nucleic Acid Atoms
Solvent Atoms622
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing