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Crystal structure of ferrous deoxymyoglobin at pH 6.8
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 AND 5-10% OF GLYCEROL PH 6.8)
Crystal Properties Matthews coefficient Solvent content 1.46 15.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.9 α = 90 b = 28.75 β = 105.72 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 110 IMAGE PLATE MARRESEARCH 2004-07-10 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 1.25 33.9 97.1 0.05 2.34 2.62 33121
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 1.25 1.32 95.5 0.18 4.18 2.27
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GJN 1.25 26.78 31498 1675 97.2 0.136 0.134 0.164 0.1906 RANDOM 16.38
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] -0.29 0.03 0.12 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.122 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 11.406 r_dihedral_angle_1_deg 4.112 r_scangle_it 3.799 r_scbond_it 2.818 r_mcangle_it 2.796 r_mcbond_it 2.096 r_angle_refined_deg 0.979 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.122 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 11.406 r_dihedral_angle_1_deg 4.112 r_scangle_it 3.799 r_scbond_it 2.818 r_mcangle_it 2.796 r_mcbond_it 2.096 r_angle_refined_deg 0.979 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.22 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.085 r_bond_refined_d 0.005 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 193 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling