3RRA

Crystal structure of enolase PRK14017 (target EFI-500653) from Ralstonia pickettii 12J with magnesium bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RR1PDB entry 3RR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52940.1M TRIS-HCL, 200MM AMMONIUM ACETATE, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.339α = 90
b = 117.339β = 90
c = 113.685γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 315MIRRORS2009-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.35094.80.0957.24.334611-548.346
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)
12.32.3492.80.91.24.1

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 DIFFRACTIONMRTHROUGHOUTPDB entry 3RR12.35031342102894.460.207630.20580.26258RANDOM66.691
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]
-34.05-34.0568.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_3_deg16.52
r_dihedral_angle_4_deg14.431
r_scangle_it12.936
r_scbond_it9.053
r_mcangle_it5.957
r_dihedral_angle_1_deg5.403
r_mcbond_it3.967
r_angle_refined_deg1.118
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_3_deg16.52
r_dihedral_angle_4_deg14.431
r_scangle_it12.936
r_scbond_it9.053
r_mcangle_it5.957
r_dihedral_angle_1_deg5.403
r_mcbond_it3.967
r_angle_refined_deg1.118
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5794
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms4

Software

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