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Crystal structure of oxidized Symerythrin from Cyanophora paradoxa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5.5 279 PEG3350, NH4Cl, BisTris, pH 5.5, hanging drop, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.593 α = 90 b = 81.593 β = 90 c = 46.277 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 CCD ADSC Q315R 2010-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.976 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.2 30.6 100 0.079 0.079 23.4 17.8 107444 107444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.25 100 0.335 0.335 6.3 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1RYT 1.2 30.6 107444 102004 5397 99.92 0.10188 0.10067 0.0983 0.12453 0.1197 RANDOM 10.462
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.679 r_sphericity_free 22.754 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_3_deg 13.698 r_scangle_it 11.749 r_sphericity_bonded 9.835 r_scbond_it 8.787 r_mcangle_it 5.52 r_dihedral_angle_1_deg 5.304 r_rigid_bond_restr 4.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.679 r_sphericity_free 22.754 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_3_deg 13.698 r_scangle_it 11.749 r_sphericity_bonded 9.835 r_scbond_it 8.787 r_mcangle_it 5.52 r_dihedral_angle_1_deg 5.304 r_rigid_bond_restr 4.412 r_mcbond_it 4.199 r_angle_refined_deg 3.625 r_angle_other_deg 3.014 r_mcbond_other 2.005 r_chiral_restr 0.272 r_gen_planes_refined 0.021 r_bond_refined_d 0.019 r_gen_planes_other 0.012 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2756 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 4
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction PHENIX phasing