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AGAO covalent complex with Tranylcypromine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AV4 PDB ENTRY 1AV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A SINGLE CRYSTAL WAS SOAKED WITH TCP BY SLOWLY ADDING TCP TO THE DROP TO ACHIEVE A 100 FOLD EXCESS OF TCP OVER ENZYME ACTIVE SITES. THE CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL, WITH THE CONCENTRAION OF TCP BEING MAINTAINED CONSTANT. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS.
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.113 α = 90 b = 63.001 β = 112.04 c = 184.49 γ = 90
Symmetry Space Group I 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 MARRESEARCH OSMIC MIRRORS 2003-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.65 28.25 98.2 0.06 15.73 7.4 200663 -3 22.32
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 1.65 1.67 80 0.46 3
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 1AV4 1.65 28.28 190611 10049 99.2 0.172 0.171 0.1736 0.199 0.1988 RANDOM 17.34
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] -1.93 0.04 2.82 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.392 r_scangle_it 5.984 r_scbond_it 4.17 r_mcangle_it 2.872 r_mcbond_it 1.897 r_angle_refined_deg 1.405 r_angle_other_deg 0.88 r_symmetry_vdw_other 0.256 r_nbd_other 0.252 r_nbd_refined 0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.392 r_scangle_it 5.984 r_scbond_it 4.17 r_mcangle_it 2.872 r_mcbond_it 1.897 r_angle_refined_deg 1.405 r_angle_other_deg 0.88 r_symmetry_vdw_other 0.256 r_nbd_other 0.252 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.091 r_symmetry_hbond_refined 0.09 r_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 9738 Nucleic Acid Atoms Solvent Atoms 1034 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling