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M.acetivorans protoglobin in complex with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VEB PDB ENTRY 2VEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% PEG 4000, 10% ISOPROPANOL, 0.1 M HEPES PH 7.0, 0.02 M POTASSIUM FERRICYANIDE, 0.01 M KCN
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.15 α = 90 b = 47.96 β = 106.66 c = 80.29 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 26.32 94.2 0.1 10.4 4.1 44547 1
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 93.1 0.16 7 4.1
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 2VEB 1.6 25.84 41953 2238 93.07 0.17808 0.17485 0.172 0.23831 0.2349 RANDOM 11.031
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] 0.15 0.03 -0.06 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 18.471 r_dihedral_angle_3_deg 14.351 r_sphericity_free 11.937 r_sphericity_bonded 6.194 r_dihedral_angle_1_deg 5.692 r_scangle_it 4.808 r_scbond_it 3.368 r_mcangle_it 2.19 r_rigid_bond_restr 1.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 18.471 r_dihedral_angle_3_deg 14.351 r_sphericity_free 11.937 r_sphericity_bonded 6.194 r_dihedral_angle_1_deg 5.692 r_scangle_it 4.808 r_scbond_it 3.368 r_mcangle_it 2.19 r_rigid_bond_restr 1.721 r_angle_refined_deg 1.605 r_mcbond_it 1.411 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3191 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing