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Structure of PETN reductase Y186F in complex with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 25%(w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid(pH 6.2), 17%(v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.618 α = 90 b = 68.664 β = 90 c = 88.602 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 4 2003-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9 ESRF ID14-1
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 1 15 98.2 0.087 11.1 4.2 172733 169624
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 1.03 84 0.489 1.9 3.1
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 1VYR 1 14.37 172733 169624 8938 98.2 0.13924 0.13924 0.1384 0.1448 0.15486 0.1463 RANDOM 10.713
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] -0.57 0.82 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.705 r_dihedral_angle_4_deg 14.115 r_dihedral_angle_3_deg 11.898 r_dihedral_angle_1_deg 5.809 r_sphericity_free 4.392 r_sphericity_bonded 2.878 r_scangle_it 2.752 r_scbond_it 1.882 r_angle_refined_deg 1.513 r_mcangle_it 1.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.705 r_dihedral_angle_4_deg 14.115 r_dihedral_angle_3_deg 11.898 r_dihedral_angle_1_deg 5.809 r_sphericity_free 4.392 r_sphericity_bonded 2.878 r_scangle_it 2.752 r_scbond_it 1.882 r_angle_refined_deg 1.513 r_mcangle_it 1.501 r_angle_other_deg 1.2 r_mcbond_it 1.004 r_rigid_bond_restr 0.934 r_mcbond_other 0.496 r_symmetry_vdw_refined 0.476 r_symmetry_vdw_other 0.343 r_nbd_other 0.259 r_nbd_refined 0.254 r_symmetry_hbond_refined 0.237 r_xyhbond_nbd_refined 0.136 r_nbtor_other 0.087 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2716 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing