☰ Navigation Tabs
Trp(60)B9Ala mutation of 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 1.93 36.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.51 α = 90 b = 47.66 β = 107.22 c = 80.22 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 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 1.7 29.86 99.8 0.11 8.7 4 38690 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 1.7 1.79 100 0.41 3.1 4
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 1.7 28.36 36740 1937 99.82 0.15206 0.14876 0.1484 0.21487 0.2129 RANDOM 12.991
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] -0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_4_deg 21.197 r_dihedral_angle_3_deg 13.288 r_sphericity_free 11.465 r_scangle_it 7.164 r_sphericity_bonded 6.557 r_dihedral_angle_1_deg 6.499 r_scbond_it 5.269 r_rigid_bond_restr 3.601 r_mcangle_it 3.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_4_deg 21.197 r_dihedral_angle_3_deg 13.288 r_sphericity_free 11.465 r_scangle_it 7.164 r_sphericity_bonded 6.557 r_dihedral_angle_1_deg 6.499 r_scbond_it 5.269 r_rigid_bond_restr 3.601 r_mcangle_it 3.475 r_mcbond_it 2.588 r_angle_refined_deg 1.221 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 3192 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing