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Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, rhomobohedral form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XRG PDB entry 1XRG modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 290 INDEX 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 coefficient Solvent content 1.69 27.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.546 α = 90 b = 78.546 β = 90 c = 89.18 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.2 54.09 99.1 0.047 6 32783 32477
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.2 1.27 94 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1XRG modified with CCP4 program CHAINSAW 1.2 54.085 32783 32453 1647 0.107 0.107 0.106 0.1169 0.131 0.1382 RANDOM 8.16
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.862 r_dihedral_angle_3_deg 10.133 r_dihedral_angle_4_deg 9.22 r_scangle_it 6.511 r_dihedral_angle_1_deg 6.507 r_scbond_it 4.537 r_mcbond_other 2.965 r_mcangle_it 2.909 r_rigid_bond_restr 2.42 r_angle_refined_deg 2.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.862 r_dihedral_angle_3_deg 10.133 r_dihedral_angle_4_deg 9.22 r_scangle_it 6.511 r_dihedral_angle_1_deg 6.507 r_scbond_it 4.537 r_mcbond_other 2.965 r_mcangle_it 2.909 r_rigid_bond_restr 2.42 r_angle_refined_deg 2.206 r_mcbond_it 2.162 r_angle_other_deg 1.266 r_chiral_restr 0.134 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_gen_planes_other 0.009 r_bond_other_d 0.006 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 Atoms Number Protein Atoms 919 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 14
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling