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
2.141.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.369α = 90
b = 41.442β = 104.049
c = 72.133γ = 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
11.23096.20.0680.0730.0270.99829.87.473208
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)
11.21.2292.90.6690.720.2630.8563.67.3

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-VALUE5YUK1.23073183374896.1180.1140.11280.141814.193
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]
-0.032-0.0650.0590.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.123
r_dihedral_angle_2_deg33.682
r_dihedral_angle_4_deg23.139
r_sphericity_bonded13.443
r_dihedral_angle_3_deg11.742
r_dihedral_angle_1_deg7.093
r_lrange_it6.289
r_rigid_bond_restr6.079
r_lrange_other5.583
r_mcangle_other4.514
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.123
r_dihedral_angle_2_deg33.682
r_dihedral_angle_4_deg23.139
r_sphericity_bonded13.443
r_dihedral_angle_3_deg11.742
r_dihedral_angle_1_deg7.093
r_lrange_it6.289
r_rigid_bond_restr6.079
r_lrange_other5.583
r_mcangle_other4.514
r_mcangle_it4.504
r_scangle_it4.014
r_scangle_other4.013
r_mcbond_it3.379
r_scbond_it3.281
r_scbond_other3.281
r_mcbond_other3.181
r_angle_refined_deg2.423
r_angle_other_deg1.209
r_symmetry_nbd_refined0.312
r_nbd_refined0.303
r_nbd_other0.231
r_chiral_restr0.194
r_symmetry_nbd_other0.188
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_refined0.157
r_xyhbond_nbd_refined0.13
r_symmetry_nbtor_other0.086
r_metal_ion_refined0.07
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_symmetry_xyhbond_nbd_other0.008
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms13

Software

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