X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0841.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.399α = 90
b = 41.285β = 104.027
c = 71.917γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9793PAL/PLS7A (6B, 6C1)

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
11.23096.60.0860.0930.0340.98920.77.573023
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)
11.21.2293.80.3310.3560.1310.9427.67.4

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5YUK1.23073007373496.5680.1180.11630.14111.725
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]
-0.027-0.06-0.0330.081
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.176
r_dihedral_angle_2_deg34.555
r_dihedral_angle_4_deg25.794
r_sphericity_bonded12.63
r_dihedral_angle_3_deg12.469
r_rigid_bond_restr6.715
r_dihedral_angle_1_deg6.575
r_lrange_it4.824
r_lrange_other4.175
r_scangle_it3.621
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.176
r_dihedral_angle_2_deg34.555
r_dihedral_angle_4_deg25.794
r_sphericity_bonded12.63
r_dihedral_angle_3_deg12.469
r_rigid_bond_restr6.715
r_dihedral_angle_1_deg6.575
r_lrange_it4.824
r_lrange_other4.175
r_scangle_it3.621
r_scangle_other3.62
r_scbond_it3.213
r_scbond_other3.213
r_angle_refined_deg2.6
r_mcangle_other2.37
r_mcangle_it2.342
r_mcbond_it1.772
r_mcbond_other1.708
r_angle_other_deg1.34
r_nbd_other0.343
r_symmetry_nbd_refined0.307
r_nbd_refined0.281
r_metal_ion_refined0.272
r_symmetry_nbd_other0.204
r_chiral_restr0.198
r_nbtor_refined0.187
r_symmetry_xyhbond_nbd_refined0.172
r_xyhbond_nbd_refined0.134
r_symmetry_nbtor_other0.085
r_bond_refined_d0.032
r_gen_planes_refined0.015
r_bond_other_d0.004
r_gen_planes_other0.004
r_symmetry_xyhbond_nbd_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing