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Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% isopropanol, 0.1M Tris-HCl, pH 8.5, 13.5 % (w/v) PEG 4000, 5% glycerol, 0.01mM FAD, 0.5mM PNP
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.433 α = 90 b = 77.177 β = 90 c = 210.242 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 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.5397 SSRF BL17U
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 2.48 30 100 0.089 19.37 7.3 32252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 0.493
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 MOLECULAR REPLACEMENT THROUGHOUT 3IHG 2.48 30 30628 1558 99.43 0.1961 0.19352 0.2083 0.24576 0.2499 RANDOM 48.655
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] -1.41 1.75 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_4_deg 19.826 r_dihedral_angle_3_deg 18.571 r_long_range_B_other 11.554 r_long_range_B_refined 11.552 r_scangle_other 7.832 r_dihedral_angle_1_deg 6.372 r_mcangle_it 5.369 r_mcangle_other 5.369 r_scbond_it 4.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_4_deg 19.826 r_dihedral_angle_3_deg 18.571 r_long_range_B_other 11.554 r_long_range_B_refined 11.552 r_scangle_other 7.832 r_dihedral_angle_1_deg 6.372 r_mcangle_it 5.369 r_mcangle_other 5.369 r_scbond_it 4.936 r_scbond_other 4.936 r_mcbond_it 3.632 r_mcbond_other 3.631 r_angle_refined_deg 1.638 r_angle_other_deg 1.118 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6147 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing