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Structure of the acyl-enzyme complex of an N-terminal nucleophile (Ntn) hydrolase, OAT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VZ6 PDB ENTRY 1VZ6, CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 290 1.4M AMMONIUM SULPHATE, 100MM N-ACETYL-L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.273 α = 90 b = 73.878 β = 92.71 c = 172.166 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 IMAGE PLATE MARRESEARCH MONTEL 2007-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 2.33 37 94.2 0.12 6.4 3.7 62183 51
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 2.33 2.45 97.9 0.7 2.03 3.7
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 1VZ6, CHAIN A 2.33 171.5 58750 3048 93.66 0.25538 0.25386 0.2536 0.28432 0.2838 RANDOM 22.038
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 -1.98 -1 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.576 r_dihedral_angle_4_deg 23.531 r_dihedral_angle_3_deg 17.326 r_dihedral_angle_1_deg 8.785 r_scangle_it 2.909 r_scbond_it 1.811 r_angle_refined_deg 1.713 r_angle_other_deg 1.331 r_mcangle_it 0.916 r_mcbond_it 0.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.576 r_dihedral_angle_4_deg 23.531 r_dihedral_angle_3_deg 17.326 r_dihedral_angle_1_deg 8.785 r_scangle_it 2.909 r_scbond_it 1.811 r_angle_refined_deg 1.713 r_angle_other_deg 1.331 r_mcangle_it 0.916 r_mcbond_it 0.768 r_symmetry_vdw_other 0.302 r_nbd_refined 0.243 r_symmetry_vdw_refined 0.243 r_symmetry_hbond_refined 0.227 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.179 r_chiral_restr 0.168 r_nbtor_other 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 r_mcbond_other r_mcangle_other r_scbond_other 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 11211 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing