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Crystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP P212121)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIL PDB ENTRY 2YIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 291 VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. VAPOR DIFFUSION, HANGING DROP. PROTEIN SOLUTION: 50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL. DROPLET: 1 MICROLITER PROTEIN SOLUTION: 1 MICROLITER RESERVOIR SOLUTION. PROTEIN:1-THIO-BETA-D-GALACTOSE MOLAR RATIO 1:100.
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.31 α = 90 b = 130 β = 90 c = 158.85 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 110 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2000-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 2.14 35 99.5 0.03 38.6 5 61346 -3 28.6
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 2.14 2.2 95.8 0.1 14.1 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2YIL 2.14 33.89 58275 3068 100 0.16086 0.15869 0.1715 0.20242 0.2083 RANDOM 29.115
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_4_deg 12.252 r_dihedral_angle_1_deg 6.532 r_scangle_it 5.936 r_scbond_it 4.003 r_mcangle_it 2.669 r_angle_refined_deg 1.905 r_mcbond_it 1.597 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_4_deg 12.252 r_dihedral_angle_1_deg 6.532 r_scangle_it 5.936 r_scbond_it 4.003 r_mcangle_it 2.669 r_angle_refined_deg 1.905 r_mcbond_it 1.597 r_angle_other_deg 0.959 r_mcbond_other 0.539 r_chiral_restr 0.12 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5985 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing