X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L2O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M CaCl2, 0.1M MgCl2, 0.1M PIPES pH7, 22.5% PEG smear
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.343α = 90
b = 149.56β = 95.428
c = 125.076γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.95374CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
13.548.1698.50.954.7346102
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.620.618

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE3.548.1646082219698.2830.2310.23020.254364.069
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]
5.759-3.753-0.466-4.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.684
r_dihedral_angle_6_deg10.535
r_dihedral_angle_1_deg5.07
r_lrange_it4.8
r_lrange_other4.8
r_mcangle_it2.655
r_mcangle_other2.655
r_dihedral_angle_2_deg2.6
r_scangle_it2.287
r_scangle_other2.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.684
r_dihedral_angle_6_deg10.535
r_dihedral_angle_1_deg5.07
r_lrange_it4.8
r_lrange_other4.8
r_mcangle_it2.655
r_mcangle_other2.655
r_dihedral_angle_2_deg2.6
r_scangle_it2.287
r_scangle_other2.287
r_mcbond_it1.518
r_mcbond_other1.518
r_scbond_it1.263
r_scbond_other1.263
r_angle_refined_deg0.667
r_angle_other_deg0.239
r_symmetry_xyhbond_nbd_refined0.236
r_nbd_other0.206
r_symmetry_nbd_refined0.204
r_nbd_refined0.174
r_symmetry_nbd_other0.169
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.118
r_symmetry_nbtor_other0.074
r_ncsr_local_group_50.055
r_ncsr_local_group_70.051
r_ncsr_local_group_110.051
r_ncsr_local_group_260.051
r_symmetry_xyhbond_nbd_other0.05
r_ncsr_local_group_130.05
r_ncsr_local_group_220.05
r_ncsr_local_group_10.049
r_ncsr_local_group_230.049
r_ncsr_local_group_270.049
r_ncsr_local_group_40.048
r_ncsr_local_group_120.048
r_ncsr_local_group_180.048
r_ncsr_local_group_250.048
r_ncsr_local_group_60.047
r_ncsr_local_group_200.047
r_ncsr_local_group_240.047
r_ncsr_local_group_170.046
r_ncsr_local_group_30.045
r_ncsr_local_group_100.045
r_ncsr_local_group_160.045
r_ncsr_local_group_20.044
r_ncsr_local_group_90.044
r_ncsr_local_group_210.044
r_ncsr_local_group_190.043
r_ncsr_local_group_280.043
r_ncsr_local_group_150.042
r_ncsr_local_group_80.041
r_ncsr_local_group_140.039
r_chiral_restr0.031
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms30496
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms356

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing