2W6N

Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J9GPDB ENTRY 2J9G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M KCL AND 2-8% PEG-800
Crystal Properties
Matthews coefficientSolvent content
2.4549.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.14α = 90
b = 105.937β = 90
c = 122.454γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDASCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
11.872095.20.0539.975.786865
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)
11.871.9468.20.325.332.9

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 2J9G1.8780.06817994303950.1770.1750.217RANDOM18.64
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]
-0.060.35-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.915
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.263
r_scangle_it2.323
r_scbond_it1.554
r_angle_refined_deg1.224
r_mcangle_it0.825
r_angle_other_deg0.777
r_mcbond_it0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.915
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.263
r_scangle_it2.323
r_scbond_it1.554
r_angle_refined_deg1.224
r_mcangle_it0.825
r_angle_other_deg0.777
r_mcbond_it0.75
r_symmetry_vdw_other0.198
r_nbd_refined0.193
r_nbd_other0.177
r_nbtor_refined0.169
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.112
r_nbtor_other0.079
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms6850
Nucleic Acid Atoms
Solvent Atoms1061
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing