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Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Strontium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.6 289 MPD, Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.81 56.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.429 α = 90 b = 95.429 β = 90 c = 63.973 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 MAR CCD 165 mm Monochromator 2008-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 3 82.64 94.9 0.068 17.2 4 11558 6442 -3
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 3 3.11 96.8 0.454 4 669
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NXQ 3 50 11558 6413 309 94.55 0.2369 0.2369 0.2347 0.2814 0.2723 RANDOM 80.4157
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] -2.68 -1.34 -2.68 4.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_4_deg 21.399 r_dihedral_angle_3_deg 21.286 r_dihedral_angle_1_deg 7.528 r_scangle_it 5.155 r_scbond_it 2.791 r_mcangle_it 1.833 r_angle_refined_deg 1.815 r_mcbond_it 0.888 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_4_deg 21.399 r_dihedral_angle_3_deg 21.286 r_dihedral_angle_1_deg 7.528 r_scangle_it 5.155 r_scbond_it 2.791 r_mcangle_it 1.833 r_angle_refined_deg 1.815 r_mcbond_it 0.888 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 996 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing