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Crystal Structure of C-Phycocyanin from Galdieria sulphuraria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 291 9.5% PEG 2000,0.1M HEPES, 0.1M MGCl2, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.818 α = 90 b = 102.818 β = 90 c = 172.883 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 315 mirrors 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97923 APS 19-ID
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 1.85 50 99.5 0.092 0.092 15.5 5.3 30304 30145 -3
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) 1.85 1.92 98.4 0.538 0.538 2.516 5.2
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 1KTP 1.85 10 28415 1521 99.52 0.18466 0.18205 0.1911 0.23127 0.2407 RANDOM 27.185
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] -2.04 -1.02 -2.04 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.527 r_dihedral_angle_4_deg 15.954 r_dihedral_angle_3_deg 15.091 r_dihedral_angle_1_deg 4.851 r_scangle_it 4.013 r_scbond_it 2.655 r_angle_refined_deg 2.298 r_mcangle_it 1.33 r_mcbond_it 0.865 r_symmetry_hbond_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.527 r_dihedral_angle_4_deg 15.954 r_dihedral_angle_3_deg 15.091 r_dihedral_angle_1_deg 4.851 r_scangle_it 4.013 r_scbond_it 2.655 r_angle_refined_deg 2.298 r_mcangle_it 1.33 r_mcbond_it 0.865 r_symmetry_hbond_refined 0.321 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.283 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.215 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2464 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing ARP model building WARP model building