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The monoclinic structure of phycocyanin from Gloeobacter violaceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VJR PDB ENTRY 2VJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8% PEG 4000, 0.1 M NA ACETATE PH 4.6 MIXED WITH IN EQUAL VOLUME OF 10MG/ML PROTEIN SOLUTION, HANGING DROP VAPOUR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.877 α = 90 b = 142.04 β = 107.65 c = 115.313 γ = 90
Symmetry Space Group P 1 21 1
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 2.4 43.44 98.9 0.11 8.94 3.63 102846 44.82
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 2.4 2.42 93.7 0.33 1.71 3.08
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 2VJR 2.4 109.76 102819 5148 98.8 0.194 0.192 0.1931 0.218 0.2184 RANDOM 28.18
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] 0.371 -1.261 -0.716 -0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 14.709 r_dihedral_angle_1_deg 5.417 r_scangle_it 2.605 r_angle_refined_deg 2.056 r_scbond_it 1.699 r_mcangle_it 0.87 r_mcbond_it 0.813 r_symmetry_hbond_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 14.709 r_dihedral_angle_1_deg 5.417 r_scangle_it 2.605 r_angle_refined_deg 2.056 r_scbond_it 1.699 r_mcangle_it 0.87 r_mcbond_it 0.813 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.168 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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_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 15216 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 774
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing