2VPQ

Crystal structure of biotin carboxylase from S. aureus complexed with AMPPNP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M KCL; 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2945.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.247α = 90
b = 63.318β = 103.82
c = 105.142γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-08-13MSINGLE 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
12.15093.80.148.073.255214
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)
12.12.1870.10.431.92.3

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 1DV22.12052269281094.10.2190.2150.284RANDOM19.18
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]
0.35-0.21-1.681.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.811
r_dihedral_angle_3_deg16.201
r_dihedral_angle_4_deg15.623
r_dihedral_angle_1_deg6.009
r_scangle_it1.79
r_angle_refined_deg1.231
r_scbond_it1.181
r_angle_other_deg0.885
r_mcangle_it0.707
r_mcbond_it0.608
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.811
r_dihedral_angle_3_deg16.201
r_dihedral_angle_4_deg15.623
r_dihedral_angle_1_deg6.009
r_scangle_it1.79
r_angle_refined_deg1.231
r_scbond_it1.181
r_angle_other_deg0.885
r_mcangle_it0.707
r_mcbond_it0.608
r_symmetry_vdw_other0.246
r_symmetry_vdw_refined0.204
r_nbd_refined0.194
r_nbd_other0.192
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.175
r_nbtor_refined0.171
r_nbtor_other0.084
r_chiral_restr0.07
r_bond_refined_d0.009
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 Atoms6967
Nucleic Acid Atoms
Solvent Atoms817
Heterogen Atoms68

Software

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