X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000
Crystal Properties
Matthews coefficientSolvent content
3.4464.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.936α = 90.016
b = 108.867β = 90
c = 134.726γ = 83.304
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300-HS2021-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9830980.0590.0670.03125.64.6398402
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0596.80.7930.4292.14.3

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-VALUE7XQA1.98228.7283794361844793.170.2130.21150.234732.657
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]
-0.127-0.1810.0550.096-0.028-0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.003
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.959
r_lrange_it7.137
r_lrange_other7.032
r_dihedral_angle_1_deg6.789
r_scangle_it4.959
r_scangle_other4.959
r_mcangle_it3.809
r_mcangle_other3.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.003
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.959
r_lrange_it7.137
r_lrange_other7.032
r_dihedral_angle_1_deg6.789
r_scangle_it4.959
r_scangle_other4.959
r_mcangle_it3.809
r_mcangle_other3.809
r_scbond_it3.162
r_scbond_other3.162
r_mcbond_it2.546
r_mcbond_other2.546
r_angle_refined_deg1.426
r_angle_other_deg1.312
r_nbd_other0.324
r_symmetry_nbd_refined0.218
r_symmetry_nbd_other0.196
r_nbd_refined0.195
r_symmetry_xyhbond_nbd_refined0.195
r_xyhbond_nbd_refined0.168
r_nbtor_refined0.155
r_chiral_restr_other0.127
r_symmetry_nbtor_other0.081
r_chiral_restr0.068
r_symmetry_xyhbond_nbd_other0.065
r_ncsr_local_group_60.058
r_ncsr_local_group_20.057
r_ncsr_local_group_240.057
r_ncsr_local_group_150.056
r_ncsr_local_group_50.049
r_ncsr_local_group_70.049
r_ncsr_local_group_10.048
r_ncsr_local_group_30.048
r_ncsr_local_group_100.048
r_ncsr_local_group_120.048
r_ncsr_local_group_230.048
r_ncsr_local_group_250.048
r_ncsr_local_group_260.048
r_ncsr_local_group_80.047
r_ncsr_local_group_190.047
r_ncsr_local_group_210.047
r_ncsr_local_group_280.047
r_ncsr_local_group_160.046
r_ncsr_local_group_180.046
r_ncsr_local_group_130.045
r_ncsr_local_group_140.045
r_ncsr_local_group_90.044
r_ncsr_local_group_270.044
r_ncsr_local_group_200.043
r_xyhbond_nbd_other0.03
r_ncsr_local_group_170.012
r_ncsr_local_group_40.01
r_ncsr_local_group_110.009
r_bond_refined_d0.008
r_ncsr_local_group_220.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29184
Nucleic Acid Atoms
Solvent Atoms2759
Heterogen Atoms472

Software

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