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Crystal structure of oxy-hemoglobin from Brycon cephalus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQ5 PDB ENTRY 1XQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.366 α = 90 b = 54.039 β = 113.89 c = 101.906 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 100 CCD MAR CCD 165 mm 2005-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.437 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 19.89 20385
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XQ5 2.4 19.89 19316 1042 86.93 0.17175 0.1662 0.1643 0.27944 0.2731 RANDOM 39.582
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 0.04 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.272 r_dihedral_angle_3_deg 22.082 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_1_deg 9.657 r_scangle_it 5.383 r_scbond_it 3.687 r_angle_refined_deg 2.713 r_mcangle_it 2.264 r_mcbond_it 1.298 r_symmetry_hbond_refined 0.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.272 r_dihedral_angle_3_deg 22.082 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_1_deg 9.657 r_scangle_it 5.383 r_scbond_it 3.687 r_angle_refined_deg 2.713 r_mcangle_it 2.264 r_mcbond_it 1.298 r_symmetry_hbond_refined 0.378 r_symmetry_vdw_refined 0.355 r_metal_ion_refined 0.348 r_nbtor_refined 0.331 r_nbd_refined 0.283 r_chiral_restr 0.217 r_xyhbond_nbd_refined 0.181 r_bond_refined_d 0.029 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4502 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing