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X-ray crystal structure of Pseudoazurin Met16Phe/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, SITTING DROP 7.5 293 Buffer for crystallization: 0.1 M sodium acetate pH 4.5
Precipitant: 30 % PEG1500
Soaking (Cryoprotectant): 0.1 M Tris-HCl pH 7.5, 40 % PEG1500
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.17 α = 90 b = 41.16 β = 98.71 c = 34.83 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 ADSC QUANTUM 210 2017-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.192 46.048 92.3 0.072 0.079 0.033 12.5 5.4 38384
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 1.192 1.223 87.3 0.317 4.4 5.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BQK 1.19 46.05 36446 1936 92.03 0.12965 0.12792 0.16116 0.1698 RANDOM 13.494
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.745 r_sphericity_free 30.995 r_dihedral_angle_3_deg 16.694 r_sphericity_bonded 9.296 r_dihedral_angle_4_deg 7.716 r_dihedral_angle_1_deg 6.964 r_rigid_bond_restr 5.942 r_long_range_B_refined 4.69 r_long_range_B_other 3.201 r_scangle_other 3.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.745 r_sphericity_free 30.995 r_dihedral_angle_3_deg 16.694 r_sphericity_bonded 9.296 r_dihedral_angle_4_deg 7.716 r_dihedral_angle_1_deg 6.964 r_rigid_bond_restr 5.942 r_long_range_B_refined 4.69 r_long_range_B_other 3.201 r_scangle_other 3.158 r_scbond_other 2.965 r_scbond_it 2.96 r_angle_refined_deg 2.771 r_mcangle_other 1.903 r_mcangle_it 1.864 r_mcbond_it 1.493 r_mcbond_other 1.435 r_angle_other_deg 1.256 r_chiral_restr 0.192 r_bond_refined_d 0.033 r_gen_planes_refined 0.013 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 918 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SCALA data scaling iMOSFLM data processing PDB_EXTRACT data extraction MOLREP phasing