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Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloroform bound to the XE4 cavity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SDH PDB ENTRY 3SDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 296 1.5-2.5M PHOSPHATE BUFFER, PH 7.50, SMALL TUBES, TEMPERATURE 298K, Microbatch, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.536 α = 90 b = 43.487 β = 122.25 c = 82.853 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2005-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 0.91 46.3 77.9 0.075 0.075 20 4 205646 160199
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) 0.91 1.01 59.3 0.189 0.189 4.7 2.1
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 (All) 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 FREE R PDB ENTRY 3SDH 0.91 46.3 152165 160199 8034 75.8 0.1288 0.1288 0.1288 0.1305 0.1555 0.1528 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 34 2315.44 2761.87
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.085 s_anti_bump_dis_restr 0.046 s_similar_adp_cmpnt 0.034 s_from_restr_planes 0.0236 s_angle_d 0.022 s_non_zero_chiral_vol 0.016 s_zero_chiral_vol 0.015 s_bond_d 0.007 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2424 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 98
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing