5FNC

Dynamic Undocking and the Quasi-Bound State as tools for Drug Design


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WI6PDB ENTRY 2WI6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7955.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.872α = 90
b = 90.285β = 90
c = 98.332γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 100MIRRORS2014-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER D8 VENTURE TXS GENERATOR

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
12.266.5199.50.0811.174.27154012
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)
12.22.2496.30.322.942.94

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 2WI62.220.521463476799.460.193580.191180.24039RANDOM26.659
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]
0.020.17-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.571
r_dihedral_angle_4_deg21.05
r_dihedral_angle_3_deg14.89
r_dihedral_angle_1_deg6.816
r_angle_refined_deg1.92
r_angle_other_deg0.885
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.571
r_dihedral_angle_4_deg21.05
r_dihedral_angle_3_deg14.89
r_dihedral_angle_1_deg6.816
r_angle_refined_deg1.92
r_angle_other_deg0.885
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.008
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
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 Atoms1628
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
AMoREphasing