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
3.3763.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.31α = 90.009
b = 106.404β = 90.013
c = 135.541γ = 96.214
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300-HS2022-05-18MSINGLE 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
12.053098.20.0810.0930.04517.54.3352119
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)
12.052.1296.80.6170.7120.3522.43.9

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-VALUE7XQA2.05229.9193479631760396.9080.1890.18760.208229.873
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]
-0.039-0.0160.0460.2050.128-0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.282
r_dihedral_angle_3_deg15.633
r_dihedral_angle_4_deg13.492
r_dihedral_angle_1_deg6.63
r_lrange_it6.132
r_lrange_other6.092
r_scangle_it4.551
r_scangle_other4.551
r_mcangle_it3.117
r_mcangle_other3.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.282
r_dihedral_angle_3_deg15.633
r_dihedral_angle_4_deg13.492
r_dihedral_angle_1_deg6.63
r_lrange_it6.132
r_lrange_other6.092
r_scangle_it4.551
r_scangle_other4.551
r_mcangle_it3.117
r_mcangle_other3.117
r_scbond_it2.882
r_scbond_other2.882
r_mcbond_it2.09
r_mcbond_other2.09
r_angle_refined_deg1.488
r_angle_other_deg1.344
r_chiral_restr_other1.157
r_nbd_other0.296
r_symmetry_nbd_refined0.202
r_nbd_refined0.191
r_symmetry_nbd_other0.178
r_nbtor_refined0.155
r_xyhbond_nbd_refined0.141
r_symmetry_xyhbond_nbd_refined0.133
r_chiral_restr0.079
r_symmetry_nbtor_other0.078
r_ncsr_local_group_20.06
r_ncsr_local_group_150.06
r_ncsr_local_group_60.059
r_ncsr_local_group_240.059
r_ncsr_local_group_10.052
r_ncsr_local_group_100.052
r_ncsr_local_group_140.051
r_ncsr_local_group_160.051
r_ncsr_local_group_260.051
r_ncsr_local_group_50.05
r_ncsr_local_group_70.05
r_ncsr_local_group_80.05
r_ncsr_local_group_120.05
r_ncsr_local_group_210.05
r_ncsr_local_group_230.05
r_ncsr_local_group_250.05
r_ncsr_local_group_180.049
r_ncsr_local_group_280.049
r_ncsr_local_group_30.048
r_ncsr_local_group_90.048
r_ncsr_local_group_190.048
r_ncsr_local_group_270.048
r_ncsr_local_group_200.047
r_ncsr_local_group_130.046
r_ncsr_local_group_110.013
r_ncsr_local_group_220.013
r_ncsr_local_group_170.011
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_ncsr_local_group_40.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29136
Nucleic Acid Atoms
Solvent Atoms1827
Heterogen Atoms744

Software

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