2W6O | pdb_00002w6o

Crystal structure of Biotin carboxylase from E. coli in complex with 4-Amino-7,7-dimethyl-7,8-dihydro-quinazolinone fragment


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4148.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.629α = 90
b = 113.367β = 90
c = 121.737γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE 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
12.510088.40.114.454.6129998
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)
12.52.59900.472.933.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J9G2.51528116152088.70.2340.230.220.308RANDOM32.81
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]
3.66-1.44-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.686
r_dihedral_angle_4_deg16.756
r_dihedral_angle_3_deg16.751
r_dihedral_angle_1_deg5.453
r_scangle_it1.838
r_angle_refined_deg1.132
r_scbond_it1.106
r_mcangle_it0.826
r_mcbond_it0.466
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.686
r_dihedral_angle_4_deg16.756
r_dihedral_angle_3_deg16.751
r_dihedral_angle_1_deg5.453
r_scangle_it1.838
r_angle_refined_deg1.132
r_scbond_it1.106
r_mcangle_it0.826
r_mcbond_it0.466
r_nbtor_refined0.299
r_symmetry_hbond_refined0.245
r_nbd_refined0.192
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.138
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.003
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
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 Atoms6858
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms30

Software

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