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Structure of reduced PETN reductase in complex with progesterone
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 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.233 α = 90 b = 68.636 β = 90 c = 88.44 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 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 15 98.2 0.087 11.1 4.2 154638 151855
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 1.03 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 1.05 14.6 154638 151855 8019 98.2 0.12946 0.12946 0.12839 0.1327 0.15004 0.1316 RANDOM 9.61
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] 0.54 0.07 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.142 r_dihedral_angle_4_deg 16.23 r_dihedral_angle_3_deg 12.179 r_dihedral_angle_1_deg 5.913 r_sphericity_free 4.204 r_scangle_it 2.575 r_sphericity_bonded 2.303 r_scbond_it 1.847 r_angle_refined_deg 1.497 r_mcangle_it 1.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.142 r_dihedral_angle_4_deg 16.23 r_dihedral_angle_3_deg 12.179 r_dihedral_angle_1_deg 5.913 r_sphericity_free 4.204 r_scangle_it 2.575 r_sphericity_bonded 2.303 r_scbond_it 1.847 r_angle_refined_deg 1.497 r_mcangle_it 1.414 r_rigid_bond_restr 1.141 r_mcbond_it 1.047 r_angle_other_deg 0.854 r_mcbond_other 0.419 r_symmetry_vdw_other 0.292 r_nbd_other 0.26 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.088 r_nbtor_other 0.086 r_symmetry_vdw_refined 0.065 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2840 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing