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3D Structure of Ferric Methanosarcina Acetivorans Protoglobin I149F mutant in Aquomet form
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 VAPOR DIFFUSION 7.5 277 10% isopropanol, 20% PEG 4000, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.844 α = 90 b = 48.368 β = 102.5 c = 80.782 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 QUANTUM 315r 2007-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.2 78.81 99.6 0.112 10.5 3.6 19625
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 2.2 2.32 99.9 0.283 5.9 3.9
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 2.2 49.64 18609 1005 99.47 0.24278 0.23877 0.2393 0.31597 0.3155 RANDOM 23.777
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] 0.18 0.08 0.01 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_3_deg 19.685 r_dihedral_angle_4_deg 14.78 r_dihedral_angle_1_deg 7.937 r_scangle_it 4.284 r_scbond_it 3 r_mcangle_it 1.939 r_mcbond_it 1.183 r_angle_refined_deg 1.133 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_3_deg 19.685 r_dihedral_angle_4_deg 14.78 r_dihedral_angle_1_deg 7.937 r_scangle_it 4.284 r_scbond_it 3 r_mcangle_it 1.939 r_mcbond_it 1.183 r_angle_refined_deg 1.133 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3206 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 123
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling