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Structure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv. oryze, in complex with fragment 493
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 0.05M Cadmium sulfate, 0.1M HEPES, 2.0M Sodium acetate trihydrate, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.48 64.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.002 α = 90 b = 59.002 β = 90 c = 264.653 γ = 120
Symmetry Space Group P 61 2 2
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 210 2009-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.999 PAL/PLS 4A
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 50 97.5 21.5 7.9 19166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.1 26.95 15907 832 98.56 0.17873 0.17645 0.1763 0.22387 0.2234 RANDOM 24.993
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 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 6.922 r_long_range_B_refined 6.597 r_scbond_it 3.286 r_mcangle_it 2.873 r_mcbond_it 2.1 r_angle_refined_deg 2.042 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 6.922 r_long_range_B_refined 6.597 r_scbond_it 3.286 r_mcangle_it 2.873 r_mcbond_it 2.1 r_angle_refined_deg 2.042 r_chiral_restr 0.149 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 1323 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing