3M1X

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XRGPDB entry 1XRG modified with CCP4 program CHAINSAW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.5290INDEX SCREEN CONDITION D4: 100MM CITRATE, 25% PEG 3350, ENHIA.00579.A AT 25.8 MG/ML, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.6927.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.546α = 90
b = 78.546β = 90
c = 89.18γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-1SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.254.0999.10.04763278332477
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.27945

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 1XRG modified with CCP4 program CHAINSAW1.254.085327833245316470.1070.1070.1060.131RANDOM8.16
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.862
r_dihedral_angle_3_deg10.133
r_dihedral_angle_4_deg9.22
r_scangle_it6.511
r_dihedral_angle_1_deg6.507
r_scbond_it4.537
r_mcbond_other2.965
r_mcangle_it2.909
r_rigid_bond_restr2.42
r_angle_refined_deg2.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.862
r_dihedral_angle_3_deg10.133
r_dihedral_angle_4_deg9.22
r_scangle_it6.511
r_dihedral_angle_1_deg6.507
r_scbond_it4.537
r_mcbond_other2.965
r_mcangle_it2.909
r_rigid_bond_restr2.42
r_angle_refined_deg2.206
r_mcbond_it2.162
r_angle_other_deg1.266
r_chiral_restr0.134
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_gen_planes_other0.009
r_bond_other_d0.006
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms919
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms14

Software

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