2J9G

Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV2PDB ENTRY 1DV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M BIS-TRIS PH 6.5, 0.2M CACL2, 45% MPD
Crystal Properties
Matthews coefficientSolvent content
2.1742.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.704α = 90
b = 112.251β = 90
c = 121.769γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
12.055099.90.0829.97759125
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)
12.052.121000.564.226.7

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 1DV22.0582.4856070299099.70.1920.190.236RANDOM23.64
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]
0.460.87-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.132
r_dihedral_angle_4_deg13.74
r_dihedral_angle_3_deg12.565
r_dihedral_angle_1_deg5.117
r_scangle_it1.546
r_angle_refined_deg1.064
r_scbond_it1.032
r_angle_other_deg0.978
r_mcangle_it0.651
r_mcbond_it0.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.132
r_dihedral_angle_4_deg13.74
r_dihedral_angle_3_deg12.565
r_dihedral_angle_1_deg5.117
r_scangle_it1.546
r_angle_refined_deg1.064
r_scbond_it1.032
r_angle_other_deg0.978
r_mcangle_it0.651
r_mcbond_it0.603
r_symmetry_vdw_other0.243
r_nbd_other0.185
r_nbd_refined0.184
r_symmetry_vdw_refined0.176
r_nbtor_refined0.166
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.129
r_nbtor_other0.08
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
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 Atoms6823
Nucleic Acid Atoms
Solvent Atoms669
Heterogen Atoms70

Software

Software
Software NamePurpose
SCALEPACKdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACphasing
REFMACrefinement