X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UYS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M sodium malonate, 20 % polyethylene glycol 3350, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.7855.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.503α = 90
b = 97.918β = 93.89
c = 84.737γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.85098.4273.767599
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8386.60.57523.2

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 REPLACEMENTTHROUGHOUT3UYS1.85065536195198.410.161040.15970.2085RANDOM43.195
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]
-2.72-1.052.420.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_sphericity_bonded28.181
r_dihedral_angle_4_deg13.487
r_dihedral_angle_3_deg12.914
r_dihedral_angle_1_deg5.576
r_long_range_B_other5.041
r_long_range_B_refined5.037
r_scangle_other4.768
r_mcangle_it4.272
r_mcangle_other4.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_sphericity_bonded28.181
r_dihedral_angle_4_deg13.487
r_dihedral_angle_3_deg12.914
r_dihedral_angle_1_deg5.576
r_long_range_B_other5.041
r_long_range_B_refined5.037
r_scangle_other4.768
r_mcangle_it4.272
r_mcangle_other4.271
r_scbond_other4.167
r_scbond_it4.166
r_mcbond_it3.551
r_mcbond_other3.533
r_rigid_bond_restr2.658
r_angle_refined_deg1.226
r_angle_other_deg0.899
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4750
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
MOLREPphasing