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Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ODJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285.15 12.5 % MPD (v/v), 12.5 % PEG 1000 (w/v) , 12.5 % PEG 3350 (w/v), 0.1 MES/imidazole pH 6.5, 0.03 M sodium phosphate dibasic dihydrate, 0.03 M ammonium sulfate and 0.03 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.169 α = 90 b = 100.167 β = 95.99 c = 66.945 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2019-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.87 48.28 99.1 0.095 0.104 0.041 0.997 15.2 6.6 67224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.92 91.7 0.776 0.844 0.327 0.837 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ODJ 1.87 48.28 63811 3384 99.13 0.1639 0.1623 0.1941 0.1904 RANDOM 29.952
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] 1.72 0.17 -1.69 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 16.477 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 7.1 r_angle_refined_deg 2.378 r_angle_other_deg 1.057 r_chiral_restr 0.149 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 16.477 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 7.1 r_angle_refined_deg 2.378 r_angle_other_deg 1.057 r_chiral_restr 0.149 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5893 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction