X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IGD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529170% MPD, 100 mM ZnSO4, 100 mM NaCI
Crystal Properties
Matthews coefficientSolvent content
2.8256.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.452α = 90
b = 75.621β = 90
c = 51.153γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
11.142.3794.60.0770.9979.353.47213389739647
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)
11.11.1768.70.7880.8111.352.2857166

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 REPLACEMENTTHROUGHOUT1IGD1.142.37106704561595.980.126450.125470.14501RANDOM16.87
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]
-1.13-0.371.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.094
r_sphericity_free30.902
r_sphericity_bonded15.671
r_dihedral_angle_3_deg12.348
r_rigid_bond_restr6.61
r_dihedral_angle_1_deg6.527
r_long_range_B_refined4.053
r_long_range_B_other4.053
r_scangle_other3.394
r_scbond_it3.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.094
r_sphericity_free30.902
r_sphericity_bonded15.671
r_dihedral_angle_3_deg12.348
r_rigid_bond_restr6.61
r_dihedral_angle_1_deg6.527
r_long_range_B_refined4.053
r_long_range_B_other4.053
r_scangle_other3.394
r_scbond_it3.033
r_scbond_other3.031
r_mcangle_it2.552
r_mcangle_other2.551
r_mcbond_it2.003
r_mcbond_other1.933
r_angle_refined_deg1.389
r_angle_other_deg0.702
r_chiral_restr0.153
r_bond_refined_d0.034
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_4_deg
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1800
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
ADDREFdata reduction
Aimlessdata scaling
REFMACphasing