X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Sodium malonate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7254.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.11α = 90
b = 90.107β = 90
c = 126.479γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2022-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.185099.90.1310.9989.747465239
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.3199.53.060.5760.727

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-VALUE2.18248.88335271178399.8780.2060.20330.2569.667
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]
3.0491.911-4.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.502
r_dihedral_angle_6_deg17.502
r_lrange_it11.884
r_lrange_other11.883
r_scangle_it9.496
r_scangle_other9.495
r_mcangle_it7.535
r_mcangle_other7.533
r_scbond_it6.427
r_scbond_other6.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.502
r_dihedral_angle_6_deg17.502
r_lrange_it11.884
r_lrange_other11.883
r_scangle_it9.496
r_scangle_other9.495
r_mcangle_it7.535
r_mcangle_other7.533
r_scbond_it6.427
r_scbond_other6.425
r_dihedral_angle_1_deg5.927
r_mcbond_other5.261
r_mcbond_it5.26
r_dihedral_angle_2_deg2.427
r_angle_refined_deg1.275
r_angle_other_deg0.421
r_nbd_other0.26
r_nbd_refined0.218
r_symmetry_nbd_other0.212
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.154
r_ncsr_local_group_10.154
r_symmetry_nbd_refined0.128
r_symmetry_xyhbond_nbd_refined0.112
r_symmetry_nbtor_other0.077
r_chiral_restr0.06
r_symmetry_xyhbond_nbd_other0.011
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3767
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XDSdata scaling
PHASERphasing