X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62930,2M Imidazole Malate pH6 30% PEG 4K
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.552α = 90
b = 71.358β = 90
c = 94.954γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.91976ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
1241.899.80.1340.1340.1730.1080.9897.34.5990032203313.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.80.7480.7480.9760.6190.6032.14.3

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 REPLACEMENTTHROUGHOUT3GPG241.820700127899.640.1960.193860.23108RANDOM27.891
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]
-3.42-0.383.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.419
r_dihedral_angle_3_deg12.708
r_dihedral_angle_4_deg12.357
r_dihedral_angle_1_deg5.694
r_long_range_B_refined4.722
r_long_range_B_other4.6
r_angle_refined_deg1.304
r_scangle_other0.971
r_mcangle_it0.936
r_mcangle_other0.936
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.419
r_dihedral_angle_3_deg12.708
r_dihedral_angle_4_deg12.357
r_dihedral_angle_1_deg5.694
r_long_range_B_refined4.722
r_long_range_B_other4.6
r_angle_refined_deg1.304
r_scangle_other0.971
r_mcangle_it0.936
r_mcangle_other0.936
r_angle_other_deg0.899
r_scbond_it0.566
r_scbond_other0.563
r_mcbond_it0.525
r_mcbond_other0.524
r_chiral_restr0.07
r_bond_refined_d0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2386
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing