4GRD

Crystal structure of Phosphoribosylaminoimidazole carboxylase catalytic subunit from Burkholderia cenocepacia J2315


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XMP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9289EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 0.1 M BICINE (PH 9.0), 10% (V/V) MPD. 20% ETHYLENE GLYCOL CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
2.8857.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.51α = 90
b = 117.18β = 90
c = 122.31γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.977408ALS5.0.1

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
11.851000.08916.2871473-322.7
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)
11.851.91000.513.7

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 REPLACEMENTTHROUGHOUT1XMP1.8548.1227147136180.1480.1470.176RANDOM12.97
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]
-0.29-0.40.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.679
r_dihedral_angle_4_deg21.028
r_dihedral_angle_3_deg12.357
r_dihedral_angle_1_deg5.6
r_angle_refined_deg1.351
r_angle_other_deg0.944
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.679
r_dihedral_angle_4_deg21.028
r_dihedral_angle_3_deg12.357
r_dihedral_angle_1_deg5.6
r_angle_refined_deg1.351
r_angle_other_deg0.944
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4908
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement