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Crystal structure of O-acetylserine dependent cystathionine beta-synthase from Helicobacter pylori.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 Peg20K-Peg550MME 15%, 0.09M Amino acids mixture, 0.1M Mes-Imadazole buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.405 α = 90 b = 82.719 β = 90 c = 96.141 γ = 90
Symmetry Space Group P 2 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 IMAGE PLATE MAR scanner 300 mm plate 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.978 ESRF BM14
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 1.9 50 100 0.117 47 16.3 45368
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 1.9 1.93 0.862
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 1Z7W 1.9 48.12 43044 2279 99.77 0.18447 0.18322 0.1966 0.20751 0.2166 RANDOM 37.455
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] 1.47 2.03 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 16.639 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_1_deg 6.668 r_long_range_B_refined 5.277 r_long_range_B_other 5.264 r_scangle_other 3.952 r_scbond_it 2.683 r_scbond_other 2.683 r_mcangle_it 2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 16.639 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_1_deg 6.668 r_long_range_B_refined 5.277 r_long_range_B_other 5.264 r_scangle_other 3.952 r_scbond_it 2.683 r_scbond_other 2.683 r_mcangle_it 2.271 r_mcangle_other 2.271 r_mcbond_it 1.526 r_mcbond_other 1.524 r_angle_refined_deg 1.469 r_angle_other_deg 0.917 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing