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X-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.10 M Hepes, 0.20 M magnesium chloride and 9.0 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.03 α = 90 b = 189.13 β = 90 c = 208.13 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2019-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 94.744 92.5 0.199 0.255 0.119 0.981 2.7 4.4 217082
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 79.6 1.8 0.061 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3brp 1.8 94.744 216823 11108 98.661 0.223 0.2211 0.2275 0.2682 0.269 30.779
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] 1.698 -1.668 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 17.181 r_dihedral_angle_3_deg 15.401 r_lrange_it 6.244 r_lrange_other 6.169 r_dihedral_angle_1_deg 5.659 r_scangle_it 5.131 r_scangle_other 5.131 r_scbond_it 3.4 r_scbond_other 3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 17.181 r_dihedral_angle_3_deg 15.401 r_lrange_it 6.244 r_lrange_other 6.169 r_dihedral_angle_1_deg 5.659 r_scangle_it 5.131 r_scangle_other 5.131 r_scbond_it 3.4 r_scbond_other 3.4 r_mcangle_other 3.303 r_mcangle_it 3.302 r_mcbond_it 2.384 r_mcbond_other 2.38 r_angle_refined_deg 1.598 r_angle_other_deg 1.413 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.19 r_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.161 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.009 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 14874 Nucleic Acid Atoms Solvent Atoms 1215 Heterogen Atoms 788
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction autoPROC data scaling PHASER phasing