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Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I87 PDB ENTRY 2I87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 283 25% PEG3350, 0.2M lithium sulfate monohydrate, 0.1M bis-Tris, pH5.5, sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.351 α = 90 b = 78.351 β = 90 c = 300.989 γ = 90
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 ADSC QUANTUM 270 2008-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 100 44441 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 100
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 (All) 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 2I87 2.8 42.26 42154 42154 2238 99.98 0.21957 0.21957 0.21559 0.218 0.29549 0.2958 RANDOM 52.296
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.494 r_dihedral_angle_3_deg 22.215 r_dihedral_angle_4_deg 20.566 r_dihedral_angle_1_deg 7.542 r_scangle_it 2.955 r_scbond_it 1.82 r_angle_refined_deg 1.806 r_mcangle_it 1.392 r_mcbond_it 0.77 r_symmetry_hbond_refined 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.494 r_dihedral_angle_3_deg 22.215 r_dihedral_angle_4_deg 20.566 r_dihedral_angle_1_deg 7.542 r_scangle_it 2.955 r_scbond_it 1.82 r_angle_refined_deg 1.806 r_mcangle_it 1.392 r_mcbond_it 0.77 r_symmetry_hbond_refined 0.428 r_nbtor_refined 0.317 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10559 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing