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Full length structure of cystathionine beta-synthase from Drosophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M54 PDB entry 1M54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 23% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.914 α = 90 b = 138.157 β = 90 c = 75.192 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2009-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 1.8 50 95.9 0.08 12.4 8 44821 42962
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) 1.8 1.86 72.2 0.403 5.8 3209
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 1M54 1.8 41.26 44821 41020 2186 95.66 0.1612 0.1595 0.1683 0.1932 0.1959 RANDOM 20.0323
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 13.642 r_dihedral_angle_1_deg 5.585 r_scangle_it 3.864 r_scbond_it 2.341 r_mcangle_it 1.55 r_angle_refined_deg 1.348 r_mcbond_it 0.842 r_angle_other_deg 0.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 13.642 r_dihedral_angle_1_deg 5.585 r_scangle_it 3.864 r_scbond_it 2.341 r_mcangle_it 1.55 r_angle_refined_deg 1.348 r_mcbond_it 0.842 r_angle_other_deg 0.706 r_mcbond_other 0.219 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3826 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 58
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction BALBES phasing