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Crystal structure of radiation-induced metmyoglobin - aqua ferrous myoglobin at pH 5.2
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 5.2 BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 5-10% OF GLYCEROL PH 5.2)
Crystal Properties Matthews coefficient Solvent content 1.47 32.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.192 α = 90 b = 28.688 β = 105.81 c = 35.557 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 2003-11-23 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 30.43 98.2 0.04 9.71 2.52 29762
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 98.8 0.18 3.75 2.26
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 30.4 28240 1493 97.5 0.133 0.131 0.1515 0.165 0.1537 RANDOM 15.98
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] -0.66 -0.03 0.13 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.456 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 10.936 r_dihedral_angle_1_deg 4.128 r_scangle_it 3.299 r_mcangle_it 2.737 r_scbond_it 2.299 r_mcbond_it 1.94 r_angle_refined_deg 0.975 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.456 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 10.936 r_dihedral_angle_1_deg 4.128 r_scangle_it 3.299 r_mcangle_it 2.737 r_scbond_it 2.299 r_mcbond_it 1.94 r_angle_refined_deg 0.975 r_nbtor_refined 0.327 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.185 r_chiral_restr 0.081 r_bond_refined_d 0.054 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 184 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling