2Q01 | pdb_00002q01

Crystal structure of glucuronate isomerase from Caulobacter crescentus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JS5PDB entry 1JS5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22941.0 M Sodium-potassium phosphate, pH 8.2, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.9969.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.332α = 90
b = 190.176β = 90
c = 319.29γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2006-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97960APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.345092.70.1880.1782.72.511231511231545
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.4361.90.60.570.41.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1JS52.34209970899708303591.690.199720.199720.198180.20.251250.25RANDOM51.199
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]
1.73-1.980.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.594
r_dihedral_angle_3_deg18.542
r_dihedral_angle_4_deg14.513
r_scangle_it12.408
r_scbond_it9.075
r_mcangle_it7.327
r_dihedral_angle_1_deg5.519
r_mcbond_it4.984
r_angle_refined_deg1.177
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.594
r_dihedral_angle_3_deg18.542
r_dihedral_angle_4_deg14.513
r_scangle_it12.408
r_scbond_it9.075
r_mcangle_it7.327
r_dihedral_angle_1_deg5.519
r_mcbond_it4.984
r_angle_refined_deg1.177
r_nbtor_refined0.3
r_symmetry_hbond_refined0.192
r_metal_ion_refined0.163
r_xyhbond_nbd_refined0.155
r_nbd_refined0.141
r_symmetry_vdw_refined0.089
r_chiral_restr0.087
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11530
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms3

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling