2W6Q

Crystal structure of Biotin carboxylase from E. coli in complex with the triazine-2,4-diamine fragment


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M KCL AND 2-8% PEG-800
Crystal Properties
Matthews coefficientSolvent content
2.5351.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.996α = 90
b = 105.573β = 90
c = 122.045γ = 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
12.0510096.90.0816.223.9966405
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)
12.052.1294.90.52.54

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 2J9G2.051662953336496.90.1860.1840.224RANDOM27.21
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]
0.020.48-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_4_deg18.413
r_dihedral_angle_3_deg13.666
r_dihedral_angle_1_deg5.148
r_scangle_it2.202
r_scbond_it1.308
r_angle_refined_deg1.057
r_mcangle_it0.819
r_mcbond_it0.475
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_4_deg18.413
r_dihedral_angle_3_deg13.666
r_dihedral_angle_1_deg5.148
r_scangle_it2.202
r_scbond_it1.308
r_angle_refined_deg1.057
r_mcangle_it0.819
r_mcbond_it0.475
r_nbtor_refined0.294
r_symmetry_vdw_refined0.198
r_nbd_refined0.178
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.12
r_chiral_restr0.076
r_bond_refined_d0.008
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 Atoms6860
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing