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Light harvesting protein from RC of Chlorobium tepidum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BCL PDB ENTRY 4BCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.6M hexanediol, 0.2M magnesium chloride, 0.1M HEPES pH 7.5, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.695 α = 90 b = 167.695 β = 90 c = 167.695 γ = 90
Symmetry Space Group I 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV Osmic multilayer mirrors 1999-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 2.3 118.68 99.7 0.068 0.068 24.8 4.5 18219 18207 50
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 2.3 2.38 99.8 0.64 0.64 2.4 4.5 1780
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4BCL 2.3 44.82 18174 18174 920 99.7 0.17838 0.17363 0.1808 0.27328 RANDOM 55.462
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.756 r_dihedral_angle_3_deg 19.169 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_1_deg 7.629 r_mcangle_it 3.703 r_scangle_it 3.466 r_angle_refined_deg 3.309 r_scbond_it 2.747 r_mcbond_it 2.638 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.756 r_dihedral_angle_3_deg 19.169 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_1_deg 7.629 r_mcangle_it 3.703 r_scangle_it 3.466 r_angle_refined_deg 3.309 r_scbond_it 2.747 r_mcbond_it 2.638 r_nbtor_refined 0.313 r_nbd_refined 0.243 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.124 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 2798 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 505
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing