3KRS

Structure of Triosephosphate Isomerase from Cryptosporidium Parvum at 1.55A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VFDPDB entry 2VFD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290MD PACT SCREEN G8: 20% PEG 3350, 100MM BISTRISPROPANE PH 7.5, 200MM NA2SO4, CRPAA.01119.A AT 75 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.56α = 90
b = 71.93β = 106.47
c = 75.83γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976484ALS5.0.3

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
11.5520990.07712.933.68014379305-316.19
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)
11.551.5991.30.3642.92.35877

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2VFD1.552079284792843990990.1590.1590.1570.188RANDOM9.94
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]
0.980.44-0.69-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_dihedral_angle_3_deg12.634
r_dihedral_angle_4_deg12.043
r_dihedral_angle_1_deg6.041
r_scangle_it3.839
r_scbond_it2.362
r_angle_refined_deg1.415
r_mcangle_it1.25
r_angle_other_deg0.911
r_mcbond_it0.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_dihedral_angle_3_deg12.634
r_dihedral_angle_4_deg12.043
r_dihedral_angle_1_deg6.041
r_scangle_it3.839
r_scbond_it2.362
r_angle_refined_deg1.415
r_mcangle_it1.25
r_angle_other_deg0.911
r_mcbond_it0.716
r_mcbond_other0.225
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3803
Nucleic Acid Atoms
Solvent Atoms845
Heterogen Atoms14

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling