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Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with fragment 134
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 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.528 α = 90 b = 58.528 β = 90 c = 264.214 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 2010-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.99 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 2.2 50 99 16.8 4.9 14538
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.2 30.4 13777 729 99.44 0.20953 0.20696 0.25945 0.2258 RANDOM 35.594
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] -0.02 -0.02 -0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_4_deg 15.928 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 7.333 r_scbond_it 4.526 r_mcangle_it 4.117 r_mcbond_it 2.935 r_angle_refined_deg 2.146 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_4_deg 15.928 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 7.333 r_scbond_it 4.526 r_mcangle_it 4.117 r_mcbond_it 2.935 r_angle_refined_deg 2.146 r_chiral_restr 0.145 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 1262 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing