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Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JF2 PDB ENTRY 1JF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 modified microbatch 7.5 277 1.5 M tri-sodium citrate, 0.1 M Na-HEPES, pH 7.5, modified microbatch, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.445 α = 90 b = 53.445 β = 90 c = 144.032 γ = 90
Symmetry Space Group P 41 21 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 BRUKER SMART 6000 Rigaku/msc HiRes2 2002-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.96 72.46 1 0.06 9.37 14.91 15775 -3 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.05 0.97 0.19 2.11 1982
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JF2 1.96 50 14823 780 98.51 0.22459 0.22278 0.25922 RANDOM 16.388
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] 0.42 0.42 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.924 r_scangle_it 3.421 r_scbond_it 2.156 r_mcangle_it 1.288 r_angle_refined_deg 1.207 r_mcbond_it 0.698 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.924 r_scangle_it 3.421 r_scbond_it 2.156 r_mcangle_it 1.288 r_angle_refined_deg 1.207 r_mcbond_it 0.698 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.162 r_metal_ion_refined 0.133 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 1489 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction LSCALE data scaling