X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QZ1PDB ID: 3QZ1 (One molecule of the protein alone)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529112 mg/mL protein, 0.05 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES), 0.1 M ammonium sulfate and 12.5% (w/v) polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.1342.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.383α = 90
b = 86.86β = 102.11
c = 108.923γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9782APS21-ID-G

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
12.643010010.27.5402995
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.643.421001.47.1

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 REPLACEMENTTHROUGHOUTPDB ID: 3QZ1 (One molecule of the protein alone)2.643037210308799.470.234850.231030.28084RANDOM42.618
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]
0.19-0.32-0.730.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg20.459
r_dihedral_angle_3_deg19.016
r_dihedral_angle_1_deg5.936
r_long_range_B_refined4.035
r_mcangle_it1.818
r_angle_refined_deg1.521
r_mcbond_it1.01
r_scbond_it0.908
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg20.459
r_dihedral_angle_3_deg19.016
r_dihedral_angle_1_deg5.936
r_long_range_B_refined4.035
r_mcangle_it1.818
r_angle_refined_deg1.521
r_mcbond_it1.01
r_scbond_it0.908
r_chiral_restr0.098
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10735
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing