7MGU

Improved ligand discovery using micro-beam data collection at the edge of protein crystals


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2881.6 M Sodium Citrate pH 11.2 0.3 M Sodium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.3647.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.41α = 90
b = 38.99β = 107.64
c = 57.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.92010NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.454.4299.830.99919.076.75636603
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.440.922

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 REPLACEMENTTHROUGHOUT2JIC1.454.4236603191899.830.129630.128720.14698RANDOM14.141
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]
0.46-0.03-0.28-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.891
r_dihedral_angle_4_deg14.721
r_dihedral_angle_3_deg10.211
r_long_range_B_refined9.063
r_dihedral_angle_1_deg7.684
r_long_range_B_other7.528
r_scangle_other3.665
r_scbond_it2.644
r_scbond_other2.642
r_angle_refined_deg2.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.891
r_dihedral_angle_4_deg14.721
r_dihedral_angle_3_deg10.211
r_long_range_B_refined9.063
r_dihedral_angle_1_deg7.684
r_long_range_B_other7.528
r_scangle_other3.665
r_scbond_it2.644
r_scbond_other2.642
r_angle_refined_deg2.312
r_mcangle_other1.623
r_mcangle_it1.606
r_mcbond_it1.13
r_angle_other_deg1.126
r_mcbond_other1.08
r_chiral_restr0.148
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms1480
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing