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M.acetivorans protoglobin in complex with azide
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 7.5 30% PEG 4000, 0.2 M LITHIUM SULPHATE, 0.1 M HEPES PH 7.5, 0.01 M POTASSIUM FERRICYANIDE, 0.1 M SODIUM AZIDE
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.88 α = 90 b = 48.82 β = 122.6 c = 80.59 γ = 90
Symmetry Space Group C 1 2 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 ID14-4 ESRF ID14-4
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 1.8 41.62 97.1 0.08 8.4 3.5 35389 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 1.8 1.9 97.5 0.4 3.4 3.5
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 1.8 32.91 33606 1782 96.59 0.19256 0.1892 0.1909 0.25627 0.2577 RANDOM 26.745
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] 0.01 -0.01 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 13.34 r_sphericity_free 5.284 r_dihedral_angle_1_deg 5.256 r_scangle_it 3.512 r_sphericity_bonded 2.855 r_scbond_it 2.424 r_mcangle_it 1.644 r_rigid_bond_restr 1.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 13.34 r_sphericity_free 5.284 r_dihedral_angle_1_deg 5.256 r_scangle_it 3.512 r_sphericity_bonded 2.855 r_scbond_it 2.424 r_mcangle_it 1.644 r_rigid_bond_restr 1.579 r_angle_refined_deg 1.447 r_mcbond_it 1.035 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 3182 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing