2W6Z | pdb_00002w6z

Crystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine 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
2.6653.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.482α = 90
b = 106.895β = 90
c = 122.413γ = 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
11.98077.40.0629.585.8267879
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)
11.91.9781.20.354.765.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J9G1.92064336340777.20.1860.1850.190.22RANDOM23.48
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]
-0.610.86-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.023
r_dihedral_angle_4_deg18.015
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg4.911
r_scangle_it1.974
r_scbond_it1.332
r_angle_other_deg1.215
r_angle_refined_deg1.109
r_mcangle_it0.784
r_mcbond_it0.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.023
r_dihedral_angle_4_deg18.015
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg4.911
r_scangle_it1.974
r_scbond_it1.332
r_angle_other_deg1.215
r_angle_refined_deg1.109
r_mcangle_it0.784
r_mcbond_it0.715
r_symmetry_vdw_other0.238
r_nbd_refined0.19
r_nbd_other0.178
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.113
r_symmetry_hbond_refined0.092
r_chiral_restr0.087
r_symmetry_vdw_refined0.083
r_nbtor_other0.081
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms6860
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms17

Software

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