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Crystal structure of a putative S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with S-adenosyl-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SO4 PDB entry 3SO4 modified with CCP4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 290 Microlytics MCSG1 screen, g11: 100mM Na2HPO4/citric acid pH 4.2, 40% PEG 300; CrhoA.00729.a.B1.PW37315 at 28.4mg/ml + 2.5mM S-Adenosyl-Methionine; tray 247830, puck QJI2-2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.86 α = 90 b = 117.86 β = 90 c = 54.04 γ = 120
Symmetry Space Group P 32 2 1
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 RAYONIX MX-225 2013-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.6 50 99.5 0.058 14.33 3.7 57078 56815 -3 24.262
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 1.6 1.64 99.5 0.56 2.39
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 (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 3SO4 modified with CCP4 program chainsaw 1.6 50 57078 56815 2803 99.53 0.1456 0.1445 0.1567 0.1652 0.1747 RANDOM 20.8199
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] 0.11 0.05 0.11 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 16.476 r_dihedral_angle_3_deg 12.14 r_dihedral_angle_1_deg 6.013 r_angle_refined_deg 1.645 r_mcangle_it 1.392 r_mcbond_it 0.845 r_mcbond_other 0.845 r_angle_other_deg 0.824 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 16.476 r_dihedral_angle_3_deg 12.14 r_dihedral_angle_1_deg 6.013 r_angle_refined_deg 1.645 r_mcangle_it 1.392 r_mcbond_it 0.845 r_mcbond_other 0.845 r_angle_other_deg 0.824 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2934 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 42
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction