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AGAO covalent complex with Benzylhydrazine
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 CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. FOLLOWING CRYOPROTECTION, THE CRYSTAL WAS SOAKED FOR 15 MINUTES IN CRYOPROTECTANT WITH THE ADDITION OF 2 MILLIMOLAR BENZYLHYDRAZINE DIHYDROCHLORIDE (SIGMA). THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM.
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.126 α = 90 b = 62.665 β = 112.07 c = 92.283 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 MARRESEARCH OSMIC MIRRORS 2003-03-25 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 1.86 29.86 94.2 0.06 9.46 3.033 65983 -3 25.31
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 1.86 1.93 83 0.41 2.13 2.69
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 1.86 29.85 62669 3312 94.2 0.154 0.152 0.1585 0.187 0.1921 RANDOM 18.11
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] -1.14 1 1.23 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.491 r_scangle_it 6.49 r_scbond_it 4.631 r_mcangle_it 3.23 r_mcbond_it 2.164 r_angle_refined_deg 1.465 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.315 r_nbd_other 0.249 r_nbd_refined 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.491 r_scangle_it 6.49 r_scbond_it 4.631 r_mcangle_it 3.23 r_mcbond_it 2.164 r_angle_refined_deg 1.465 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.315 r_nbd_other 0.249 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.094 r_nbtor_other 0.083 r_bond_refined_d 0.013 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 4877 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling