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Formyl-methionine-alanine complex structure of peptide deformylase from Xanthomoonas oryzae pv. oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 0.05M cadmium sulfate, 0.1M HEPES pH 7.5, 2.0M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.584 α = 90 b = 58.584 β = 90 c = 266.188 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 2009-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.99999 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 2.1 50 99.6 16778 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) 1 2.1 2.14 96.9
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 4FR8 2.2 40.35 13852 729 98.98 0.19244 0.19022 0.1979 0.23547 0.2398 RANDOM 29.755
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 0.01 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_4_deg 18.9 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 7.014 r_long_range_B_refined 6.967 r_long_range_B_other 6.967 r_scangle_other 4.884 r_scbond_it 3.252 r_mcangle_other 3.128 r_scbond_other 3.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_4_deg 18.9 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 7.014 r_long_range_B_refined 6.967 r_long_range_B_other 6.967 r_scangle_other 4.884 r_scbond_it 3.252 r_mcangle_other 3.128 r_scbond_other 3.115 r_mcangle_it 2.877 r_mcbond_it 1.913 r_mcbond_other 1.894 r_angle_refined_deg 1.856 r_angle_other_deg 0.923 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1317 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling