4AHS

Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BI4PDB ENTRY 1BI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
2.9558.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.183α = 90
b = 71.183β = 90
c = 66.653γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2008-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

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
11.7561.796.50.0716.24.9368241
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)
11.751.8480.90.451.92.6

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 1BI41.7561.6634485184195.290.207630.205530.24787RANDOM25.24
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]
0.250.130.25-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.922
r_dihedral_angle_4_deg18.621
r_dihedral_angle_3_deg16.665
r_dihedral_angle_1_deg6.36
r_angle_refined_deg2.242
r_chiral_restr0.144
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.922
r_dihedral_angle_4_deg18.621
r_dihedral_angle_3_deg16.665
r_dihedral_angle_1_deg6.36
r_angle_refined_deg2.242
r_chiral_restr0.144
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms2336
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing