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Crystal Structure determination of goat hemoglobin (Capra hircus) at 3 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D1A PDB ENTRY 3d1a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2micro litres of Hb with 2micro litre of well solution containing 25mM of Phosphate buffer at pH 7.5 with 0.5M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.678 α = 90 b = 66.896 β = 90 c = 157.593 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 3 30 89.7 0.1854 2.9 4.12 10705 9607 3 2
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) 3 3.11 93 0.5361 0.7 3.55
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3d1a 3 22.08 10705 9607 1036 89.6 0.21906 0.21269 0.2109 0.27796 0.249 RANDOM 34.953
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] 0.03 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_4_deg 16.899 r_dihedral_angle_1_deg 8.682 r_scangle_it 3.003 r_angle_refined_deg 2.095 r_scbond_it 2.033 r_mcangle_it 1.268 r_mcbond_it 0.888 r_symmetry_vdw_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_4_deg 16.899 r_dihedral_angle_1_deg 8.682 r_scangle_it 3.003 r_angle_refined_deg 2.095 r_scbond_it 2.033 r_mcangle_it 1.268 r_mcbond_it 0.888 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.326 r_nbd_refined 0.309 r_xyhbond_nbd_refined 0.224 r_symmetry_hbond_refined 0.178 r_chiral_restr 0.116 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4389 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 172
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling