1KTG

Crystal Structure of a C. elegans Ap4A Hydrolase Binary Complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293PEG 4000, Magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.563α = 90
b = 36.758β = 114.16
c = 68.941γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87SRSPX9.6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.82096.562050240192
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8496.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KT91.819240102279312170.189770.187960.22289RANDOM7.117
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]
-0.25-0.060.3-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.396
r_dihedral_angle_1_deg4.301
r_scangle_it1.883
r_angle_refined_deg1.261
r_scbond_it1.248
r_mcangle_it0.715
r_angle_other_deg0.656
r_mcbond_it0.411
r_nbd_refined0.223
r_symmetry_hbond_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.396
r_dihedral_angle_1_deg4.301
r_scangle_it1.883
r_angle_refined_deg1.261
r_scbond_it1.248
r_mcangle_it0.715
r_angle_other_deg0.656
r_mcbond_it0.411
r_nbd_refined0.223
r_symmetry_hbond_refined0.199
r_nbd_other0.197
r_symmetry_vdw_other0.174
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.145
r_chiral_restr0.072
r_xyhbond_nbd_other0.02
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbtor_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 Atoms2099
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms44

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling