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Structure of the amidase domain of allophanate hydrolase from Pseudomonas sp strain ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DQN PDB ENTRY 2DQN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 PROTEIN AT 5.5 MG/ML WAS ADDED TO THE RESERVOIR CONDITION OF 11-14% (W/V) PEG 3350, 2% TACSIMATE PH 5. MICROSEEDS WERE ALSO ADDED TO THESE DROPS FOR REPRODUCIBLE CRYSTALS.
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.447 α = 90 b = 179.232 β = 106.63 c = 112.61 γ = 90
Symmetry Space Group P 1 21 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 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 2.5 179.2 100 0.15 12.6 7.7 107970
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 2.5 2.64 100 0.81 2.8 7.7
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 2DQN 2.5 40 102548 5385 100 0.22577 0.22405 0.2264 0.25883 0.2624 RANDOM 44.009
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] 1.24 0.42 -1.62 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.911 r_dihedral_angle_4_deg 20.165 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 6.596 r_mcangle_it 5.76 r_mcbond_it 3.767 r_mcbond_other 3.765 r_scbond_it 3.565 r_angle_refined_deg 1.315 r_angle_other_deg 1.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.911 r_dihedral_angle_4_deg 20.165 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 6.596 r_mcangle_it 5.76 r_mcbond_it 3.767 r_mcbond_other 3.765 r_scbond_it 3.565 r_angle_refined_deg 1.315 r_angle_other_deg 1.239 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20091 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing