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Pseudoazurin with engineered amicyanin ligand loop, reduced form, pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BQK PDB ENTRY 1BQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 HANGING DROP VAPOR DIFFUSION METHOD, 1 MICRO-LITER OF PROTEIN (20 MG/ML IN 100 MM MES, PH 5.5 PLUS 30 MM NACL) WAS MIXED WITH 1 MICO-L OF RESERVOIR SOLUTION (100 MM MES, PH 5.5 PLUS 2 M AMMONIUM SULFATE AND 2 M NACL). THE CRYSTALS WERE REDUCED BY ADDING 50 MM MERCAPTOETHANOL TO THE RESERVOIR SOLUTION AND BECAME COLORLESS AFTER 3 HOURS.
Crystal Properties Matthews coefficient Solvent content 2.09 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.355 α = 90 b = 105.355 β = 90 c = 56.487 γ = 120
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 CONFOCAL MAXFLUX FROM OSMIC 2007-01-09 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 1.98 50 95.6 0.06 18.5 7.1 8140 2
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 1.98 2.05 64.3 0.22 2.8 3.8
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 1BQK 1.99 30 7756 384 97 0.163 0.16 0.1864 0.23 0.2523 RANDOM 40.41
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] -1.95 -0.97 -1.95 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_3_deg 15.465 r_dihedral_angle_1_deg 6.263 r_dihedral_angle_4_deg 5.537 r_scangle_it 4.236 r_scbond_it 2.703 r_angle_refined_deg 1.556 r_mcangle_it 1.531 r_mcbond_it 1.005 r_symmetry_hbond_refined 0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_3_deg 15.465 r_dihedral_angle_1_deg 6.263 r_dihedral_angle_4_deg 5.537 r_scangle_it 4.236 r_scbond_it 2.703 r_angle_refined_deg 1.556 r_mcangle_it 1.531 r_mcbond_it 1.005 r_symmetry_hbond_refined 0.417 r_nbtor_refined 0.309 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.189 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 903 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing