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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41Q mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M6O PDB ENTRY 3M6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 12% PEG-3350, Zinc acetate 100mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.93 α = 90 b = 56.93 β = 90 c = 147.41 γ = 90
Symmetry Space Group P 43 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 2008-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.3 50 98.3 0.116 13.64 6.5 11253 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 2.3 2.44 94 0.303 5.82 5.3
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 rigid body THROUGHOUT PDB ENTRY 3M6O 2.3 28.47 10127 1126 100 0.305 0.301 0.3006 0.338 0.3359 RANDOM 25.21
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_dihedral_angle_4_deg 26.823 r_dihedral_angle_3_deg 25.268 r_dihedral_angle_1_deg 4.543 r_angle_refined_deg 2.6 r_nbtor_refined 0.329 r_nbd_refined 0.326 r_xyhbond_nbd_refined 0.319 r_symmetry_metal_ion_refined 0.314 r_symmetry_hbond_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_dihedral_angle_4_deg 26.823 r_dihedral_angle_3_deg 25.268 r_dihedral_angle_1_deg 4.543 r_angle_refined_deg 2.6 r_nbtor_refined 0.329 r_nbd_refined 0.326 r_xyhbond_nbd_refined 0.319 r_symmetry_metal_ion_refined 0.314 r_symmetry_hbond_refined 0.296 r_symmetry_vdw_refined 0.285 r_metal_ion_refined 0.238 r_chiral_restr 0.135 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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_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 1436 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling CNS phasing