X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GAGPDB ENTRY 2GAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.515% PEG 6K, 0.1 M MES (PH 6.5), 10% MPD
Crystal Properties
Matthews coefficientSolvent content
2.4850.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.76α = 90
b = 93.71β = 102.85
c = 74.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2015-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
1249.0899.90.09124.5659823
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)
122.1199.90.512.94.7

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 ENTRY 2GAG246.8562619334099.90.178550.176910.20898RANDOM25.967
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]
-0.03-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_4_deg14.369
r_dihedral_angle_3_deg13.034
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.805
r_long_range_B_other3.712
r_scangle_other1.764
r_mcangle_it1.754
r_mcangle_other1.754
r_angle_refined_deg1.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_4_deg14.369
r_dihedral_angle_3_deg13.034
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.805
r_long_range_B_other3.712
r_scangle_other1.764
r_mcangle_it1.754
r_mcangle_other1.754
r_angle_refined_deg1.137
r_scbond_it1.016
r_scbond_other1.016
r_mcbond_it1.001
r_mcbond_other1.001
r_angle_other_deg0.73
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 Atoms6888
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing