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Full length structure of cystathionine beta-synthase from Drosophila in complex with aminoacrylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PC2 PDB entry 3PC2
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 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.275 α = 90 b = 138.815 β = 90 c = 75.146 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 2010-02-07 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 1.55 50 93.8 0.1 11.2 6.6 70759 66372
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) 1.55 1.61 67.1 0.546 3.4 4714
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 PHASER THROUGHOUT PDB entry 3PC2 1.55 41.45 66337 3348 93.75 0.1503 0.1482 0.149 0.1883 0.1879 RANDOM 17.7789
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] 0.51 0.03 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.409 r_scbond_it 2.158 r_mcangle_it 1.478 r_angle_refined_deg 1.179 r_rigid_bond_restr 0.97 r_mcbond_it 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.409 r_scbond_it 2.158 r_mcangle_it 1.478 r_angle_refined_deg 1.179 r_rigid_bond_restr 0.97 r_mcbond_it 0.847 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3865 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 64
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction PHASER phasing