3M4S

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, orthorhombic form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290INDEX SCREEN CONDITION F10: 0.2 M NaCl, 25% PEG 3350, ENHIA.00579.A AT 25.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.6α = 90
b = 110.49β = 90
c = 52.92γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.329.0896.40.08514.584.82751626517-334.83
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)
12.32.36950.4982.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMR, MRTHROUGHOUT2.329275162647813530.2160.2130.273RANDOM10.6
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]
-0.29-1.131.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.706
r_dihedral_angle_3_deg14.862
r_dihedral_angle_4_deg11.472
r_dihedral_angle_1_deg6.318
r_scangle_it2.565
r_scbond_it1.555
r_angle_refined_deg1.443
r_mcangle_it0.934
r_angle_other_deg0.808
r_mcbond_it0.504
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.706
r_dihedral_angle_3_deg14.862
r_dihedral_angle_4_deg11.472
r_dihedral_angle_1_deg6.318
r_scangle_it2.565
r_scbond_it1.555
r_angle_refined_deg1.443
r_mcangle_it0.934
r_angle_other_deg0.808
r_mcbond_it0.504
r_mcbond_other0.133
r_chiral_restr0.074
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms5435
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms1

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling