2ZOA

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DXN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.343α = 90
b = 164.343β = 90
c = 164.343γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.2804APS19-ID

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
12.42599.60.10623.15.95762045.74
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5598.50.5312.44.29413

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2DXN2.424.554616293599.60.159530.15850.1789345.824
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_4_deg21.341
r_dihedral_angle_3_deg18.837
r_dihedral_angle_1_deg6.866
r_scangle_it3.668
r_scbond_it2.379
r_angle_refined_deg1.607
r_mcangle_it1.325
r_mcbond_it0.91
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_4_deg21.341
r_dihedral_angle_3_deg18.837
r_dihedral_angle_1_deg6.866
r_scangle_it3.668
r_scbond_it2.379
r_angle_refined_deg1.607
r_mcangle_it1.325
r_mcbond_it0.91
r_nbtor_refined0.307
r_symmetry_vdw_refined0.227
r_nbd_refined0.207
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.129
r_chiral_restr0.122
r_bond_refined_d0.014
r_gen_planes_refined0.006
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_refined
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 Atoms4266
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing