X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R2D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Diffraction quality crystals appeared after 1 d at 292 K
Crystal Properties
Matthews coefficientSolvent content
2.8857.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.42α = 90
b = 108.68β = 115.84
c = 78.74γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2018-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03323APS23-ID-B

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
11.663.9399.60.0330.126.54.17602221
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)
11.61.799.70.6450.9943.14.15

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 REPLACEMENTTHROUGHOUT2r2d1.663.93137203722299.760.141780.13940.1873RANDOM33.224
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]
0.22-0.260.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.844
r_sphericity_free27.542
r_sphericity_bonded21.389
r_dihedral_angle_4_deg16.892
r_dihedral_angle_3_deg13.893
r_rigid_bond_restr7.741
r_scangle_other7.572
r_scbond_it6.921
r_scbond_other6.92
r_long_range_B_refined6.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.844
r_sphericity_free27.542
r_sphericity_bonded21.389
r_dihedral_angle_4_deg16.892
r_dihedral_angle_3_deg13.893
r_rigid_bond_restr7.741
r_scangle_other7.572
r_scbond_it6.921
r_scbond_other6.92
r_long_range_B_refined6.848
r_long_range_B_other6.848
r_dihedral_angle_1_deg5.759
r_mcangle_it5.173
r_mcangle_other5.173
r_mcbond_it4.694
r_mcbond_other4.657
r_angle_other_deg0.898
r_angle_refined_deg0.696
r_chiral_restr0.037
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_bond_other_d
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 Atoms6711
Nucleic Acid Atoms
Solvent Atoms657
Heterogen Atoms213

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing