2W6P

Crystal structure of Biotin carboxylase from E. coli in complex with 5-Methyl-6-phenyl-quinazoline-2,4-diamine


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
2.7154.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.986α = 90
b = 106.475β = 90
c = 121.978γ = 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
11.8510095.50.0624.174.2389788
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)
11.851.9296.90.492.713.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J9G1.852085154448695.60.1880.1870.216RANDOM20.46
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]
0.070.26-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.775
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg12.27
r_dihedral_angle_1_deg5.098
r_scangle_it2.286
r_scbond_it1.385
r_angle_refined_deg1.081
r_mcangle_it0.894
r_angle_other_deg0.777
r_mcbond_it0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.775
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg12.27
r_dihedral_angle_1_deg5.098
r_scangle_it2.286
r_scbond_it1.385
r_angle_refined_deg1.081
r_mcangle_it0.894
r_angle_other_deg0.777
r_mcbond_it0.54
r_symmetry_vdw_other0.271
r_nbd_refined0.198
r_nbd_other0.18
r_nbtor_refined0.167
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.116
r_symmetry_hbond_refined0.11
r_nbtor_other0.078
r_chiral_restr0.065
r_bond_refined_d0.008
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 Atoms6438
Nucleic Acid Atoms
Solvent Atoms725
Heterogen Atoms19

Software

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