X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529520 mg/ml protein, PEG 4000, isopropanol, sodium acetate, potassium ferricyanate
Crystal Properties
Matthews coefficientSolvent content
2.2745.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.517α = 109.86
b = 52.567β = 92.93
c = 61.771γ = 92.2
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.36257.96292.370.05214.13.9804487654413
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)
11.3621.39866.240.582.23.8

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 REPLACEMENTTHROUGHOUT5C0Z1.36257.9676544390192.370.1310.1290.16982RANDOM21.413
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]
0.040.040.89-0.510.85-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.915
r_dihedral_angle_2_deg31.917
r_dihedral_angle_4_deg31.575
r_sphericity_bonded12.158
r_dihedral_angle_3_deg12.075
r_dihedral_angle_1_deg6.497
r_long_range_B_refined3.725
r_long_range_B_other3.046
r_rigid_bond_restr2.519
r_scangle_other2.45
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.915
r_dihedral_angle_2_deg31.917
r_dihedral_angle_4_deg31.575
r_sphericity_bonded12.158
r_dihedral_angle_3_deg12.075
r_dihedral_angle_1_deg6.497
r_long_range_B_refined3.725
r_long_range_B_other3.046
r_rigid_bond_restr2.519
r_scangle_other2.45
r_scbond_it2.042
r_scbond_other2.033
r_mcangle_it1.824
r_mcangle_other1.824
r_angle_refined_deg1.803
r_mcbond_it1.482
r_mcbond_other1.482
r_angle_other_deg1.058
r_chiral_restr0.122
r_bond_refined_d0.016
r_gen_planes_refined0.015
r_gen_planes_other0.014
r_bond_other_d0.003
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 Atoms3220
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXphasing
Aimlessdata scaling
XDSdata reduction