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The structure of phycocyanin from Gloeobacter violaceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBO PDB ENTRY 1JBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 33.3 MM LITHIUM SULFATE, 17 MM TRIS HYDROCHLORIDE PH 8.5, 5% W/V PEG 4K, MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION. HANGING DROP VAPOUR DIFFUSION.
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.538 α = 90 b = 117.538 β = 90 c = 116.163 γ = 120
Symmetry Space Group P 63 2 2
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 MARRESEARCH 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.49 29.39 99.6 0.08 34.42 21.11 16967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.51 98.8 0.41 5.56 20.96
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 PDB ENTRY 1JBO 2.6 101.53 14301 766 99.6 0.21 0.207 0.206 0.266 0.2563 RANDOM 28.22
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] -0.52 -0.26 -0.52 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_1_deg 5.738 r_angle_refined_deg 1.982 r_scangle_it 1.965 r_scbond_it 1.235 r_angle_other_deg 1.01 r_mcangle_it 0.814 r_mcbond_it 0.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_1_deg 5.738 r_angle_refined_deg 1.982 r_scangle_it 1.965 r_scbond_it 1.235 r_angle_other_deg 1.01 r_mcangle_it 0.814 r_mcbond_it 0.721 r_nbd_refined 0.23 r_symmetry_vdw_other 0.205 r_nbd_other 0.194 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.188 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.088 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2536 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing