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Sandercyanin Fluorescent Protein variant V71E bound to biliverdin IX-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 11mg/mL
0.2M calcium chloride dihydrate,
20% (w/v) PEG 3350, pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.466 α = 90 b = 38.466 β = 90 c = 117.601 γ = 90
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 MAR CCD 130 mm 2013-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 38.84 99.6 0.99 10.4 6.8 41927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.306
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5EZ2 2.5 36.56 5920 296 99.7 0.177 0.1732 0.1797 0.2535 0.2633 36.55
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] 1.079 1.079 -2.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.76 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 18.761 r_lrange_it 9.108 r_lrange_other 9.088 r_dihedral_angle_1_deg 8.435 r_scangle_it 5.991 r_scangle_other 5.988 r_mcangle_it 5.234 r_mcangle_other 5.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.76 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 18.761 r_lrange_it 9.108 r_lrange_other 9.088 r_dihedral_angle_1_deg 8.435 r_scangle_it 5.991 r_scangle_other 5.988 r_mcangle_it 5.234 r_mcangle_other 5.233 r_scbond_it 3.775 r_scbond_other 3.772 r_mcbond_it 3.379 r_mcbond_other 3.375 r_angle_refined_deg 1.613 r_angle_other_deg 1.125 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.19 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.163 r_nbd_other 0.155 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1281 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing