X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WNO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277.150.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.564.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.26α = 90
b = 109.94β = 93.775
c = 96.22γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

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
12.20985.07599.70.99916.66.688463
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)
12.2092.24799.20.7142.1

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-VALUE2.20985.07588461446699.6490.1780.1770.204340.344
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]
0.246-1.165-1.311.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.703
r_dihedral_angle_6_deg16.695
r_dihedral_angle_2_deg10.849
r_dihedral_angle_other_2_deg10.202
r_lrange_it9.143
r_lrange_other9.136
r_scangle_it7.675
r_scangle_other7.671
r_dihedral_angle_1_deg6.167
r_mcangle_it5.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.703
r_dihedral_angle_6_deg16.695
r_dihedral_angle_2_deg10.849
r_dihedral_angle_other_2_deg10.202
r_lrange_it9.143
r_lrange_other9.136
r_scangle_it7.675
r_scangle_other7.671
r_dihedral_angle_1_deg6.167
r_mcangle_it5.104
r_mcangle_other5.103
r_scbond_it4.977
r_scbond_other4.957
r_mcbond_it3.605
r_mcbond_other3.604
r_angle_refined_deg1.427
r_angle_other_deg0.478
r_nbd_refined0.221
r_xyhbond_nbd_refined0.208
r_symmetry_nbd_other0.2
r_symmetry_nbd_refined0.185
r_nbtor_refined0.182
r_nbd_other0.18
r_symmetry_xyhbond_nbd_refined0.123
r_ncsr_local_group_60.1
r_ncsr_local_group_30.098
r_ncsr_local_group_40.096
r_ncsr_local_group_10.093
r_symmetry_nbtor_other0.082
r_ncsr_local_group_20.08
r_ncsr_local_group_50.075
r_chiral_restr0.071
r_symmetry_xyhbond_nbd_other0.027
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8649
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing