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Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBQ PDB ENTRY 1JBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 18% PEG8000, 0.1 M CACODYLATE, PH 6.6 0.2 M SODIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.89 57.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.264 α = 90 b = 116.193 β = 90 c = 167.99 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 100 PIXEL DECTRIS PILATUS 6M 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 48.89 99.8 0.07 15.1 4.5 93295 2
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 2.03 99.8 0.85 2 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 1JBQ 2 95.56 88563 4662 99.64 0.17517 0.17381 0.1843 0.20068 0.2081 RANDOM 43.704
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] -1.2 1.56 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_4_deg 19.87 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 5.772 r_mcangle_it 2.261 r_scbond_it 1.873 r_angle_refined_deg 1.43 r_mcbond_it 1.388 r_mcbond_other 1.386 r_angle_other_deg 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_4_deg 19.87 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 5.772 r_mcangle_it 2.261 r_scbond_it 1.873 r_angle_refined_deg 1.43 r_mcbond_it 1.388 r_mcbond_other 1.386 r_angle_other_deg 0.804 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 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_it 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 7495 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XIA data reduction XIA data scaling PHASER phasing