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
3.3963.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.425α = 90.054
b = 107.225β = 90.04
c = 135.159γ = 83.684
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300HE2022-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

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
12.053097.40.0570.0650.031284.2354721
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1291.20.6080.6930.3312.84.3

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-VALUE7XQA2.0527.7393529171771697.4410.1990.19860.214529.249
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]
-0.033-0.029-0.0950.0550.089-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.124
r_dihedral_angle_4_deg17.675
r_dihedral_angle_3_deg15.954
r_dihedral_angle_1_deg6.591
r_lrange_it6.117
r_lrange_other6.086
r_scangle_it4.584
r_scangle_other4.584
r_mcangle_it3.15
r_mcangle_other3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.124
r_dihedral_angle_4_deg17.675
r_dihedral_angle_3_deg15.954
r_dihedral_angle_1_deg6.591
r_lrange_it6.117
r_lrange_other6.086
r_scangle_it4.584
r_scangle_other4.584
r_mcangle_it3.15
r_mcangle_other3.15
r_scbond_it2.874
r_scbond_other2.874
r_mcbond_it2.098
r_mcbond_other2.097
r_angle_refined_deg1.442
r_angle_other_deg1.307
r_nbd_other0.238
r_symmetry_nbd_refined0.22
r_nbd_refined0.193
r_symmetry_nbd_other0.188
r_nbtor_refined0.154
r_symmetry_xyhbond_nbd_refined0.145
r_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.08
r_chiral_restr0.07
r_ncsr_local_group_80.059
r_ncsr_local_group_140.058
r_ncsr_local_group_60.056
r_ncsr_local_group_150.056
r_ncsr_local_group_180.056
r_ncsr_local_group_20.054
r_ncsr_local_group_210.054
r_ncsr_local_group_160.052
r_ncsr_local_group_90.051
r_ncsr_local_group_120.051
r_ncsr_local_group_240.051
r_ncsr_local_group_280.051
r_ncsr_local_group_100.05
r_ncsr_local_group_130.05
r_ncsr_local_group_250.05
r_ncsr_local_group_10.049
r_ncsr_local_group_30.049
r_ncsr_local_group_70.049
r_ncsr_local_group_190.049
r_ncsr_local_group_260.049
r_ncsr_local_group_230.048
r_ncsr_local_group_50.045
r_ncsr_local_group_200.045
r_ncsr_local_group_270.045
r_ncsr_local_group_170.032
r_ncsr_local_group_110.031
r_ncsr_local_group_40.022
r_ncsr_local_group_220.019
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29118
Nucleic Acid Atoms
Solvent Atoms1395
Heterogen Atoms704

Software

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