3FFS

The Crystal Structure of Cryptosporidium parvum Inosine-5'-Monophosphate Dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EEPPDB entry 1EEP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298Protein solution: 4 mg/mL IMPDH, 50 mM Tris, pH 7.5, 150 mM KCl, 5 % glycerol and 2 mM dithiothreitol. Well solution: 34 % PEG 4000, 25 mM sodium acetate and 100 mM Tris-Cl, pH 8.5. Combined in a 1:1 ratio. VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.068α = 90
b = 153.319β = 90
c = 98.228γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BM0.97946APS8-BM

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
13.19501000.1796.830575
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)
3.193.311000.6326.92987

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 1EEP3.1948.343057530483153699.080.2720.2690.328RANDOM53.887
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]
0.03-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.389
r_dihedral_angle_3_deg21.72
r_dihedral_angle_4_deg20.271
r_dihedral_angle_1_deg6.239
r_angle_refined_deg1.452
r_scangle_it1.252
r_mcangle_it0.737
r_scbond_it0.737
r_mcbond_it0.409
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.389
r_dihedral_angle_3_deg21.72
r_dihedral_angle_4_deg20.271
r_dihedral_angle_1_deg6.239
r_angle_refined_deg1.452
r_scangle_it1.252
r_mcangle_it0.737
r_scbond_it0.737
r_mcbond_it0.409
r_nbtor_refined0.306
r_nbd_refined0.235
r_symmetry_vdw_refined0.178
r_xyhbond_nbd_refined0.168
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8561
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling