☰ Navigation Tabs
Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with higher solvent content and an ordered N-terminal tag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M4S PDB entry 3M4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 290 JCSG+ SCREEN CONDITION F2: 100MM CITRATE, 3150 MM AMMONIUM SULFATE, ENHIA.00579.A AT 26 MG/ML IN THE PRESENCE OF 2 MM SODIUM ORTHOVANADATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84 α = 90 b = 99.72 β = 90 c = 106.1 γ = 90
Symmetry Space Group P 21 21 21
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 2010-04-08 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 Merge 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 1.8 19.86 98.6 0.074 14.29 4.1 83127 81926 -3 23.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.85 90.9 0.424 2.7 3.2 6076
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 3M4S 1.8 19.86 83127 81664 4096 0.148 0.148 0.147 0.1526 0.183 0.1895 RANDOM 17.63
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] -0.74 -0.04 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.315 r_dihedral_angle_4_deg 11.943 r_dihedral_angle_3_deg 11.919 r_dihedral_angle_1_deg 5.661 r_scangle_it 4.551 r_scbond_it 2.777 r_angle_refined_deg 1.518 r_mcangle_it 1.463 r_mcbond_it 0.864 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.315 r_dihedral_angle_4_deg 11.943 r_dihedral_angle_3_deg 11.919 r_dihedral_angle_1_deg 5.661 r_scangle_it 4.551 r_scbond_it 2.777 r_angle_refined_deg 1.518 r_mcangle_it 1.463 r_mcbond_it 0.864 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5907 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 136
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling