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Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RL4 PDB ENTRY 1RL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 17% PEG-3350, 0.2M zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.97 α = 90 b = 55.94 β = 90 c = 148.55 γ = 90
Symmetry Space Group P 21 21 21
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 315 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.980 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 30 99 0.094 14.48 7.5 32769 32457 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.11 97.3 0.455 5.1 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RL4 2 27.97 30521 1637 99.47 0.22052 0.21703 0.28377 0.2472 RANDOM 29.745
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] 0.73 0.99 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.429 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 19.448 r_dihedral_angle_1_deg 7.109 r_scangle_it 4.006 r_scbond_it 2.897 r_angle_refined_deg 2.036 r_mcangle_it 1.77 r_mcbond_it 1.367 r_symmetry_hbond_refined 0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.429 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 19.448 r_dihedral_angle_1_deg 7.109 r_scangle_it 4.006 r_scbond_it 2.897 r_angle_refined_deg 2.036 r_mcangle_it 1.77 r_mcbond_it 1.367 r_symmetry_hbond_refined 0.419 r_symmetry_vdw_refined 0.39 r_nbtor_refined 0.319 r_xyhbond_nbd_refined 0.256 r_nbd_refined 0.244 r_metal_ion_refined 0.225 r_chiral_restr 0.141 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2830 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 11
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling