X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5277MPD 2%, Sodium Phosphate buffer pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.7755.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.184α = 90
b = 56.974β = 92.9
c = 111.136γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0723ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.4469.7199.90.0570.99914.46.640567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.5799.10.7550.3130.6666.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4IRC2.4469.7133768178899.960.222270.221050.24505RANDOM
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]
-1.87-0.05-2.814.66
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded43.067
r_dihedral_angle_2_deg33.658
r_dihedral_angle_4_deg23.32
r_dihedral_angle_3_deg19.535
r_dihedral_angle_1_deg7.405
r_rigid_bond_restr6.359
r_long_range_B_refined3.704
r_mcangle_it1.669
r_scbond_it1.393
r_angle_refined_deg1.183
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded43.067
r_dihedral_angle_2_deg33.658
r_dihedral_angle_4_deg23.32
r_dihedral_angle_3_deg19.535
r_dihedral_angle_1_deg7.405
r_rigid_bond_restr6.359
r_long_range_B_refined3.704
r_mcangle_it1.669
r_scbond_it1.393
r_angle_refined_deg1.183
r_mcbond_it0.984
r_chiral_restr0.042
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5378
Nucleic Acid Atoms1351
Solvent Atoms40
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing