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Crystal structure of peptide deformylase from Ehrlichia chaffeensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5N PDB ENTRY 1N5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 200MM AMMONIUM CITRATE, 20% PEG 3350; Protein at 28MG/ML, PH 8.5, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.26 α = 90 b = 64.43 β = 90 c = 80.91 γ = 90
Symmetry Space Group P 21 21 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 315r 2009-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9744 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 50 99.2 0.069 18.6 4.8 17813 17678 -3 42.22
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) 2.4 2.46 99.8 0.487 3.4 4.9 1291
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 PDB ENTRY 1N5N 2.4 19.67 17598 863 99 0.195 0.192 0.1875 0.246 0.2391 RANDOM 26.39
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] 0.7 0.26 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 5.755 r_scangle_it 2.939 r_scbond_it 1.742 r_angle_refined_deg 1.283 r_mcangle_it 1.039 r_angle_other_deg 0.826 r_mcbond_it 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 5.755 r_scangle_it 2.939 r_scbond_it 1.742 r_angle_refined_deg 1.283 r_mcangle_it 1.039 r_angle_other_deg 0.826 r_mcbond_it 0.535 r_mcbond_other 0.119 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2770 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 4
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling