3ESQ | pdb_00003esq

Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate phosphatase from E. Coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GMWPDB Entry 2gmw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829825% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 0.005M calcium chloride, 11% glycerol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.8132.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.904α = 90
b = 50.585β = 90
c = 52.638γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2008-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
11.740.6294.20.04713.93.64182441126.075
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)
11.71.76800.3133.22.361894

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 2gmw1.740.6211172991729994494.150.20320.200450.20.25844RANDOM29.588
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]
-1.22-0.581.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.501
r_dihedral_angle_4_deg20.815
r_dihedral_angle_3_deg12.846
r_dihedral_angle_1_deg6.729
r_scangle_it3.622
r_scbond_it2.502
r_angle_refined_deg1.504
r_mcangle_it1.376
r_mcbond_it0.885
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.501
r_dihedral_angle_4_deg20.815
r_dihedral_angle_3_deg12.846
r_dihedral_angle_1_deg6.729
r_scangle_it3.622
r_scbond_it2.502
r_angle_refined_deg1.504
r_mcangle_it1.376
r_mcbond_it0.885
r_nbtor_refined0.301
r_symmetry_vdw_refined0.248
r_symmetry_hbond_refined0.225
r_nbd_refined0.218
r_xyhbond_nbd_refined0.197
r_metal_ion_refined0.133
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms1423
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing