X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294PEG MME 2000, Sodium acetate, potassium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.9235.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.34α = 90
b = 111.1β = 105.47
c = 48.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
1255.5596.60.050.99917.33.630184
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0575.90.2090.934.62.4

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 REPLACEMENTTHROUGHOUT2gzr255.5528603155596.450.178070.175610.22198RANDOM36.902
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]
0.29-1.080.010.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.643
r_dihedral_angle_4_deg20.822
r_dihedral_angle_3_deg14.991
r_dihedral_angle_1_deg6.937
r_long_range_B_refined4.665
r_long_range_B_other4.66
r_scangle_other3.389
r_mcangle_it2.537
r_mcangle_other2.536
r_scbond_it2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.643
r_dihedral_angle_4_deg20.822
r_dihedral_angle_3_deg14.991
r_dihedral_angle_1_deg6.937
r_long_range_B_refined4.665
r_long_range_B_other4.66
r_scangle_other3.389
r_mcangle_it2.537
r_mcangle_other2.536
r_scbond_it2.19
r_scbond_other2.185
r_mcbond_it1.756
r_mcbond_other1.755
r_angle_refined_deg1.334
r_angle_other_deg0.709
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3962
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing