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
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.206α = 90
b = 41.283β = 104.184
c = 72.147γ = 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
11.23098.80.0650.070.0260.99529.77.374586
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)
11.21.2297.50.3760.1060.1510.9386.37.1

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-VALUE5YUK1.23074561382098.7680.1180.11650.140913.109
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]
-0.112-0.0250.0890.032
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.357
r_dihedral_angle_2_deg35.522
r_dihedral_angle_4_deg25.037
r_sphericity_bonded12.632
r_dihedral_angle_3_deg11.49
r_dihedral_angle_1_deg6.689
r_rigid_bond_restr5.901
r_lrange_it4.908
r_lrange_other4.617
r_scangle_it4.463
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.357
r_dihedral_angle_2_deg35.522
r_dihedral_angle_4_deg25.037
r_sphericity_bonded12.632
r_dihedral_angle_3_deg11.49
r_dihedral_angle_1_deg6.689
r_rigid_bond_restr5.901
r_lrange_it4.908
r_lrange_other4.617
r_scangle_it4.463
r_scangle_other4.462
r_scbond_it3.714
r_scbond_other3.714
r_mcangle_other2.872
r_mcangle_it2.828
r_angle_refined_deg2.437
r_mcbond_it2.187
r_mcbond_other2.149
r_angle_other_deg1.233
r_symmetry_nbd_refined0.312
r_nbd_other0.301
r_nbd_refined0.272
r_symmetry_xyhbond_nbd_refined0.229
r_chiral_restr0.192
r_nbtor_refined0.187
r_symmetry_nbd_other0.185
r_xyhbond_nbd_refined0.126
r_symmetry_nbtor_other0.086
r_metal_ion_refined0.077
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms7

Software

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