2VQD

Crystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa complexed with AMPCP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M HEPES (PH 7.0), 0.2M MGCL2, 15-20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
1.9737.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.227α = 90
b = 126.786β = 90
c = 49.878γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-05-01MSINGLE 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
12.420960.0722.95.215777
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)
12.42.4983.90.352.863.2

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 1DV22.4163.371495379195.70.1820.1780.252RANDOM33.49
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]
1.510.21-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.85
r_dihedral_angle_4_deg16.911
r_dihedral_angle_3_deg15.604
r_dihedral_angle_1_deg5.853
r_scangle_it1.503
r_angle_refined_deg1.212
r_scbond_it1.021
r_angle_other_deg0.758
r_mcangle_it0.619
r_mcbond_it0.543
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.85
r_dihedral_angle_4_deg16.911
r_dihedral_angle_3_deg15.604
r_dihedral_angle_1_deg5.853
r_scangle_it1.503
r_angle_refined_deg1.212
r_scbond_it1.021
r_angle_other_deg0.758
r_mcangle_it0.619
r_mcbond_it0.543
r_nbd_refined0.188
r_symmetry_vdw_other0.182
r_nbd_other0.176
r_symmetry_hbond_refined0.172
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.149
r_symmetry_vdw_refined0.147
r_nbtor_other0.082
r_chiral_restr0.065
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 Atoms3412
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms33

Software

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