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Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LRY pdb deposition 1lry, modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 HAMPTON RESEARCH INDEX H12: 30% PEG 2000 MME, 150MM KBR, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K; 18 hour soak in reservoir solution containing 1mM actinonin
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.25 α = 80.87 b = 65.78 β = 76.82 c = 68.29 γ = 82.75
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 RIGAKU SATURN 944+ RIGAKU VARIMAX 2012-02-07 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 2 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 99.6 0.077 0.077 17 5.8 56808 56579 -3 22.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 98 0.49 0.49 2.02 2.5 4200
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 deposition 1lry, modified with CCP4 program CHAINSAW 1.9 50 56808 56577 2852 99.6 0.185 0.185 0.182 0.1866 0.235 0.2369 RANDOM 18.66
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] -0.18 0.01 0.4 0.7 -0.1 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.807 r_dihedral_angle_4_deg 13.148 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.033 r_angle_refined_deg 1.603 r_angle_other_deg 0.924 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.807 r_dihedral_angle_4_deg 13.148 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.033 r_angle_refined_deg 1.603 r_angle_other_deg 0.924 r_chiral_restr 0.084 r_bond_refined_d 0.013 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 5570 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 117
Software Software Software Name Purpose JDirector data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling