☰ Navigation Tabs
Crystal structure of myoglobin compound III (radiation-induced)
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 CRYSTALLIZATION CONDITIONS: 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 1.5 33.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.76 α = 90 b = 28.73 β = 105.83 c = 35.44 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 IMAGE PLATE MARRESEARCH 2007-11-17 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 1.5 21.97 98.1 0.08 6.74 2.74 16256
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 1.6 1.69 99.5 0.45 1.14 2.73
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GJN 1.6 21.94 15416 785 97.5 0.169 0.167 0.209 RANDOM 16.96
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] -0.17 0.09 0.23 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.754 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 12.623 r_dihedral_angle_1_deg 4.443 r_scangle_it 2.985 r_scbond_it 1.95 r_angle_refined_deg 1.248 r_mcangle_it 1.164 r_mcbond_it 0.731 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.754 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 12.623 r_dihedral_angle_1_deg 4.443 r_scangle_it 2.985 r_scbond_it 1.95 r_angle_refined_deg 1.248 r_mcangle_it 1.164 r_mcbond_it 0.731 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.08 r_bond_refined_d 0.056 r_gen_planes_refined 0.006 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 161 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing