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Structural characterization of the hexa-coordinated globin from Spisula solidissima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 2.5 M ammonium sulfate, and 50 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.219 α = 75.65 b = 50.684 β = 88.09 c = 74.165 γ = 85.3
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 210 2007-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
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 1.7 49.01 95 0.036 24.4 3.9 70881
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 1.7 1.79 94.8 0.12 11.9 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 49.01 67301 3579 94.98 0.1522 0.14981 0.1636 0.19685 0.2052 RANDOM 16.084
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] 0.45 0.11 -0.63 -0.27 -0.24 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.677 r_dihedral_angle_3_deg 14.615 r_long_range_B_refined 6.415 r_long_range_B_other 6.003 r_dihedral_angle_1_deg 4.761 r_scangle_other 4.129 r_mcangle_it 2.973 r_mcangle_other 2.973 r_scbond_it 2.707 r_scbond_other 2.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.677 r_dihedral_angle_3_deg 14.615 r_long_range_B_refined 6.415 r_long_range_B_other 6.003 r_dihedral_angle_1_deg 4.761 r_scangle_other 4.129 r_mcangle_it 2.973 r_mcangle_other 2.973 r_scbond_it 2.707 r_scbond_other 2.707 r_mcbond_it 1.923 r_mcbond_other 1.921 r_angle_refined_deg 1.723 r_angle_other_deg 0.608 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4875 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction PHASER phasing