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
3.463.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.644α = 89.963
b = 107.875β = 90.132
c = 134.782γ = 83.438
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300-HS2022-03-11MSINGLE 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
12.1193098.20.0470.0530.025304.6322706
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)
12.122.297.10.60.680.322.54.5

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-VALUE7XQA2.11929.3933188331613396.7610.1960.19460.214831.025
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]
-0.1290.032-0.0050.1120.0820.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.404
r_dihedral_angle_3_deg15.58
r_dihedral_angle_4_deg13.409
r_dihedral_angle_1_deg6.813
r_lrange_it6.668
r_lrange_other6.668
r_scangle_it4.488
r_scangle_other4.488
r_mcangle_it3.339
r_mcangle_other3.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.404
r_dihedral_angle_3_deg15.58
r_dihedral_angle_4_deg13.409
r_dihedral_angle_1_deg6.813
r_lrange_it6.668
r_lrange_other6.668
r_scangle_it4.488
r_scangle_other4.488
r_mcangle_it3.339
r_mcangle_other3.338
r_scbond_it2.838
r_scbond_other2.838
r_mcbond_it2.185
r_mcbond_other2.184
r_angle_refined_deg1.41
r_angle_other_deg1.309
r_nbd_other0.246
r_nbd_refined0.191
r_symmetry_nbd_other0.19
r_symmetry_nbd_refined0.174
r_nbtor_refined0.155
r_xyhbond_nbd_refined0.155
r_symmetry_xyhbond_nbd_refined0.144
r_symmetry_nbtor_other0.079
r_ncsr_local_group_280.073
r_ncsr_local_group_180.072
r_chiral_restr0.067
r_ncsr_local_group_60.065
r_ncsr_local_group_210.064
r_ncsr_local_group_240.064
r_ncsr_local_group_20.062
r_ncsr_local_group_120.062
r_ncsr_local_group_140.062
r_ncsr_local_group_150.062
r_ncsr_local_group_260.062
r_ncsr_local_group_80.06
r_ncsr_local_group_160.06
r_ncsr_local_group_30.052
r_ncsr_local_group_90.051
r_ncsr_local_group_190.051
r_ncsr_local_group_200.051
r_ncsr_local_group_70.05
r_ncsr_local_group_10.049
r_ncsr_local_group_100.049
r_ncsr_local_group_130.049
r_ncsr_local_group_250.049
r_ncsr_local_group_270.049
r_ncsr_local_group_50.048
r_ncsr_local_group_230.048
r_symmetry_xyhbond_nbd_other0.037
r_ncsr_local_group_170.027
r_ncsr_local_group_220.02
r_ncsr_local_group_40.015
r_ncsr_local_group_110.01
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 Atoms28839
Nucleic Acid Atoms
Solvent Atoms2424
Heterogen Atoms720

Software

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