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Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 8.7
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 8.7 BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M TAPS AND 5-10% OF GLYCEROL PH 8.7)
Crystal Properties Matthews coefficient Solvent content 1.39 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.97 α = 90 b = 28.668 β = 105.74 c = 35.537 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 2004-02-14 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 1.18 34.3 99.1 0.04 9.36 2.55 38266
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 1.2 1.26 99.2 0.35 2.14 2.32
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 1.2 34 36234 1915 98.9 0.135 0.134 0.164 0.163 0.1814 RANDOM 13.89
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] -0.44 -0.03 -0.03 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 20.271 r_dihedral_angle_3_deg 11.092 r_scangle_it 4.196 r_dihedral_angle_1_deg 4.168 r_scbond_it 2.966 r_mcangle_it 1.929 r_mcbond_it 1.306 r_angle_refined_deg 0.95 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 20.271 r_dihedral_angle_3_deg 11.092 r_scangle_it 4.196 r_dihedral_angle_1_deg 4.168 r_scbond_it 2.966 r_mcangle_it 1.929 r_mcbond_it 1.306 r_angle_refined_deg 0.95 r_nbtor_refined 0.318 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.082 r_bond_refined_d 0.051 r_gen_planes_refined 0.01 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 214 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling