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Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryze, in complex with fragment 244
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E5D
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 3.43 64.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.661 α = 90 b = 58.661 β = 90 c = 263.749 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 2009-12-03 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 2.38 50 99.8 25 9.7 11737
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 2.38 2.42 99.1 0.43 4.5 9.1
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 MOLECULAR REPLACEMENT THROUGHOUT 5E5D 2.38 28.65 11082 555 99.73 0.18851 0.18658 0.1875 0.22693 0.2287 RANDOM 32.072
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 33.725 r_dihedral_angle_4_deg 20.561 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 7.523 r_long_range_B_refined 7.476 r_mcangle_it 4.097 r_scbond_it 4.063 r_mcbond_it 2.775 r_angle_refined_deg 2.148 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.725 r_dihedral_angle_4_deg 20.561 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 7.523 r_long_range_B_refined 7.476 r_mcangle_it 4.097 r_scbond_it 4.063 r_mcbond_it 2.775 r_angle_refined_deg 2.148 r_chiral_restr 0.13 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 1335 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing