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Crystal structure of the truncated hemoglobin from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UX8 PDB ENTRY 1UX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 PEG 5000 MME 20-25 %, ACETATE BUFFER 0.1 M PH 5.2-6.0
Crystal Properties Matthews coefficient Solvent content 1.92 35.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.123 α = 90 b = 99.339 β = 105.59 c = 35.252 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.5 40 97.5 0.02 3.6 36594
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 1.5 1.55 93.7 0.06 3.1
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 1UX8 1.5 25 34771 1824 98.4 0.168 0.167 0.1647 0.194 0.1936 RANDOM 15.82
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 -0.23 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 18.444 r_dihedral_angle_3_deg 14.884 r_dihedral_angle_1_deg 4.891 r_scangle_it 3.94 r_scbond_it 2.543 r_mcangle_it 1.857 r_angle_refined_deg 1.634 r_mcbond_it 1.157 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 18.444 r_dihedral_angle_3_deg 14.884 r_dihedral_angle_1_deg 4.891 r_scangle_it 3.94 r_scbond_it 2.543 r_mcangle_it 1.857 r_angle_refined_deg 1.634 r_mcbond_it 1.157 r_nbtor_refined 0.325 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.223 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 2080 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing