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Cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XYK PDB ENTRY 2XYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 8% PEG 8000 AND 0.1 M TRIS-HCL (PH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.91 α = 90 b = 72.25 β = 90 c = 88.31 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 100 PIXEL DECTRIS PILATUS 6M 2013-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.21 72.25 99.5 0.1 8.7 4.4 14322
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 2.21 2.33 99.7 0.45 3.1 4.6
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 2XYK 2.21 44.15 13460 714 98.42 0.1856 0.18254 0.1904 0.24617 0.2474 RANDOM 39.604
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] -0.08 0.1 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 23.451 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 6.3 r_mcangle_it 4.578 r_scbond_it 3.638 r_mcbond_it 3.047 r_mcbond_other 3.045 r_angle_refined_deg 1.752 r_angle_other_deg 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 23.451 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 6.3 r_mcangle_it 4.578 r_scbond_it 3.638 r_mcbond_it 3.047 r_mcbond_other 3.045 r_angle_refined_deg 1.752 r_angle_other_deg 0.888 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CaspR phasing