1O1Z | pdb_00001o1z

Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19.627740% (v/v) PEG-600, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 9.60
Crystal Properties
Matthews coefficientSolvent content
2.2244.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.41α = 90
b = 41.79β = 90
c = 51.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2002-10-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.98011, 0.97938, 0.97918, 0.95671APS19-BM

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
11.6501000.0562.016.7138012
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)
11.61.6695.30.19610.063.51

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.648.1836027192697.80.1410.1390.150.180.19RANDOM13.32
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]
0.06-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.05
r_dihedral_angle_4_deg19.046
r_dihedral_angle_3_deg10.828
r_scangle_it6.905
r_dihedral_angle_1_deg6.079
r_scbond_it4.411
r_mcangle_it3.054
r_mcbond_it1.79
r_angle_refined_deg1.411
r_angle_other_deg0.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.05
r_dihedral_angle_4_deg19.046
r_dihedral_angle_3_deg10.828
r_scangle_it6.905
r_dihedral_angle_1_deg6.079
r_scbond_it4.411
r_mcangle_it3.054
r_mcbond_it1.79
r_angle_refined_deg1.411
r_angle_other_deg0.882
r_symmetry_vdw_other0.336
r_symmetry_vdw_refined0.306
r_symmetry_hbond_refined0.244
r_nbd_other0.238
r_xyhbond_nbd_refined0.23
r_nbd_refined0.211
r_metal_ion_refined0.115
r_chiral_restr0.091
r_nbtor_other0.08
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1831
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building
SOLVEphasing
ARP/wARPmodel building
REFMACrefinement
RESOLVEphasing