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X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM Tris-HCl, 38% PEG4000, 40mg/mL protein
Crystal Properties Matthews coefficient Solvent content 1.91 35.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.699 α = 88.88 b = 51.227 β = 77.16 c = 57.723 γ = 86.58
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 270 2013-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
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 1.19 50 94.1 0.077 6.8 3.9 117085
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 1.19 1.21 89.7 0.342 3.6
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 1BQK 1.19 24.72 111149 5906 93.9 0.12886 0.12657 0.1323 0.17297 0.1783 RANDOM 11.281
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] 0.03 -0.02 0.1 0.04 0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.76 r_sphericity_free 18.843 r_dihedral_angle_3_deg 14.276 r_sphericity_bonded 7.818 r_dihedral_angle_4_deg 7.432 r_dihedral_angle_1_deg 7.045 r_rigid_bond_restr 4.943 r_long_range_B_refined 3.938 r_long_range_B_other 3.771 r_scangle_other 2.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.76 r_sphericity_free 18.843 r_dihedral_angle_3_deg 14.276 r_sphericity_bonded 7.818 r_dihedral_angle_4_deg 7.432 r_dihedral_angle_1_deg 7.045 r_rigid_bond_restr 4.943 r_long_range_B_refined 3.938 r_long_range_B_other 3.771 r_scangle_other 2.781 r_angle_refined_deg 2.533 r_scbond_it 2.386 r_scbond_other 2.386 r_mcangle_it 1.888 r_mcangle_other 1.888 r_mcbond_other 1.628 r_mcbond_it 1.627 r_angle_other_deg 1.192 r_chiral_restr 0.169 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3660 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction