1KA1

The PAPase Hal2p complexed with calcium and magnesium ions and reaction substrate: PAP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QGXPDB ENTRY 1QGX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529330% PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES. (Crystals were soaked in mother liquor containing 0.5 M calcium chloride for 5 hours.) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.875α = 90
b = 44.968β = 110.72
c = 72.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41999-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.8700SRSPX9.6

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
11.350.3190.30.0816.42.97317973179
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)
1.31.33477.10.452.12.6

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 1QGX1.3507317973179365490.280.134450.132610.1693RANDOM12.132
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]
-0.040.270.220.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.123
r_sphericity_free6.221
r_dihedral_angle_1_deg6.181
r_scangle_it6.143
r_sphericity_bonded5.36
r_scbond_it4.396
r_mcangle_it3.214
r_rigid_bond_restr2.631
r_mcbond_it2.399
r_angle_refined_deg1.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.123
r_sphericity_free6.221
r_dihedral_angle_1_deg6.181
r_scangle_it6.143
r_sphericity_bonded5.36
r_scbond_it4.396
r_mcangle_it3.214
r_rigid_bond_restr2.631
r_mcbond_it2.399
r_angle_refined_deg1.723
r_angle_other_deg1.253
r_nbtor_other0.383
r_xyhbond_nbd_other0.296
r_symmetry_vdw_other0.274
r_nbd_refined0.269
r_xyhbond_nbd_refined0.267
r_symmetry_vdw_refined0.259
r_symmetry_hbond_refined0.254
r_nbd_other0.225
r_chiral_restr0.113
r_metal_ion_refined0.087
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2719
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms33

Software

Software
Software NamePurpose
ADSCdata collection
SCALAdata scaling
REFMACrefinement
CCP4data scaling