☰ Navigation Tabs
Crystal structure of Sperm Whale Myoglobin mutant YQR in complex with Xenon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAZ PDB ENTRY 1NAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.7 2.6M (NH4)2SO4, 0.1M TRIS/HCL, PH8.5, pH 8.7
Crystal Properties Matthews coefficient Solvent content 2.4 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.626 α = 90 b = 90.626 β = 90 c = 45.505 γ = 120
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 MARRESEARCH 2000-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 26.1 100 0.06 15.2 5.7 28029 2 12.2
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 1.9 99.9 0.17 3.2 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1NAZ 1.6 26 2 26584 1408 100 0.165 0.1861 0.196 0.2132 RANDOM 10.55
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.579 r_dihedral_angle_4_deg 17.711 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_1_deg 4.249 r_scangle_it 3.154 r_scbond_it 2.179 r_mcangle_it 1.382 r_angle_refined_deg 1.188 r_mcbond_it 0.856 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.579 r_dihedral_angle_4_deg 17.711 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_1_deg 4.249 r_scangle_it 3.154 r_scbond_it 2.179 r_mcangle_it 1.382 r_angle_refined_deg 1.188 r_mcbond_it 0.856 r_nbtor_refined 0.314 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 1224 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing