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Crystal structure of Pseudomonas aeruginosa guanidinopropionase complexed with 1,6-diaminohexane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NIO PDB ENTRY 3NIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 297 0.1M lithium sulfate, 0.1M tri-sodium citrate at pH 5.6, 12% (w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.58 65.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 264.748 α = 90 b = 134.719 β = 104.37 c = 87.785 γ = 90
Symmetry Space Group C 1 2 1
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 2009-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.9795 PAL/PLS 4A
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 2.5 20 99.1 0.108 15.8 101621
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 PDB ENTRY 3NIO 2.5 20 96545 5070 98.91 0.19264 0.19083 0.1942 0.2269 0.227 RANDOM 26.193
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] 1.62 1.95 -0.35 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.345 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_1_deg 5.746 r_scangle_it 2.488 r_scbond_it 1.465 r_angle_refined_deg 1.298 r_mcangle_it 1.036 r_mcbond_it 0.546 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.345 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_1_deg 5.746 r_scangle_it 2.488 r_scbond_it 1.465 r_angle_refined_deg 1.298 r_mcangle_it 1.036 r_mcbond_it 0.546 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14358 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling