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Crystal structure of oxidized Symerythrin from Cyanophora paradoxa, azide adduct at 50% occupancy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 279 25% PEG 3350, 0.1M BisTris, 0.35M NH4Cl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.009 α = 90 b = 82.009 β = 90 c = 46.44 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 QUANTUM 315r 2011-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97650 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 30.74 100 0.074 18.9 12.2 68857 68857 2 2 13.96
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 1.4 1.48 100 0.441 0.441 5.6 12 10086
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 3QHB 1.4 30.74 65332 3484 99.96 0.11727 0.11517 0.1242 0.15618 0.1603 RANDOM 12.676
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] -0.74 -0.37 -0.74 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.072 r_dihedral_angle_4_deg 17.965 r_dihedral_angle_3_deg 13.672 r_sphericity_free 13.515 r_sphericity_bonded 9.286 r_scangle_it 6.801 r_dihedral_angle_1_deg 4.832 r_scbond_it 4.802 r_mcangle_it 3.304 r_mcbond_it 2.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.072 r_dihedral_angle_4_deg 17.965 r_dihedral_angle_3_deg 13.672 r_sphericity_free 13.515 r_sphericity_bonded 9.286 r_scangle_it 6.801 r_dihedral_angle_1_deg 4.832 r_scbond_it 4.802 r_mcangle_it 3.304 r_mcbond_it 2.386 r_rigid_bond_restr 2.297 r_angle_refined_deg 2.101 r_mcbond_other 1.441 r_angle_other_deg 1.142 r_chiral_restr 0.139 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 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 2730 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 10
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing