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Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GJN PDB ENTRY 1GJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 6.8)
Crystal Properties Matthews coefficient Solvent content 1.47 15.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.617 α = 90 b = 28.663 β = 105.85 c = 35.271 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 110 IMAGE PLATE MARRESEARCH 2003-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A ESRF BM1A
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 1.3 33 98.2 0.05 15.2 4 29779
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 1.3 1.37 97.3 0.42 2.8 3.7
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 1GJN 1.3 26.6 28253 1497 97.7 0.148 0.147 0.1665 0.175 0.1949 RANDOM 17.25
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] -0.3 0.2 0.18 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.824 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 10.945 r_dihedral_angle_1_deg 4.066 r_scangle_it 2.373 r_mcangle_it 2.073 r_scbond_it 1.637 r_mcbond_it 1.406 r_angle_refined_deg 1.033 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.824 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 10.945 r_dihedral_angle_1_deg 4.066 r_scangle_it 2.373 r_mcangle_it 2.073 r_scbond_it 1.637 r_mcbond_it 1.406 r_angle_refined_deg 1.033 r_nbtor_refined 0.32 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.081 r_bond_refined_d 0.055 r_gen_planes_refined 0.004 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 1199 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing