3HH5

New azaborine compounds bind to the T4 lysozyme L99A cavity - 1-ethyl-2-hydro-1,2-azaborine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92772.0-2.2M K/Na phosphase, 50mM BME, 50mM HED (vapor-diffusion for complex preparation), pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6753.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.989α = 90
b = 59.989β = 90
c = 95.466γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Si(111)2009-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03318APS23-ID-B

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
11.2522.8299.10.05334.99.5550675
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)
1.251.2788.10.1588.82.42411

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 REPLACEMENTTHROUGHOUT3DMV1.2522.8252195279798.890.163610.162640.18195RANDOM14.188
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]
0.180.090.18-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.23
r_dihedral_angle_4_deg15.722
r_dihedral_angle_3_deg11.997
r_dihedral_angle_1_deg4.777
r_sphericity_free3.191
r_rigid_bond_restr3.059
r_scangle_it3.051
r_scbond_it2.925
r_sphericity_bonded2.713
r_mcangle_it1.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.23
r_dihedral_angle_4_deg15.722
r_dihedral_angle_3_deg11.997
r_dihedral_angle_1_deg4.777
r_sphericity_free3.191
r_rigid_bond_restr3.059
r_scangle_it3.051
r_scbond_it2.925
r_sphericity_bonded2.713
r_mcangle_it1.338
r_angle_refined_deg1.167
r_mcbond_it0.773
r_nbtor_refined0.305
r_nbd_refined0.197
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.118
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1446
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms30

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling