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Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUE PDB ENTRY 1EUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 277 2M ammonium sulfate, 0.1M Na/K phosphate, 0.2M lithium sulfate, pH 6.2, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.48 α = 90 b = 56.37 β = 100.67 c = 42.56 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 210r 2009-11-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 1.0000 APS 17-BM
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 1.25 30 99 0.058 13.02 48981 48981 -3 17.458
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 1.25 1.28 93.6 0.724 1.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1EUE 1.25 18.91 48981 48981 2489 99.07 0.148 0.1468 0.1485 0.1726 0.1729 Random 12.26
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] 0.474 -0.477 -0.655 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.598 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 11.715 r_dihedral_angle_1_deg 5.275 r_scangle_it 4.906 r_scbond_it 3.416 r_scangle_other 2.682 r_mcangle_it 2.486 r_mcbond_it 1.499 r_angle_refined_deg 1.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.598 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 11.715 r_dihedral_angle_1_deg 5.275 r_scangle_it 4.906 r_scbond_it 3.416 r_scangle_other 2.682 r_mcangle_it 2.486 r_mcbond_it 1.499 r_angle_refined_deg 1.477 r_rigid_bond_restr 1.27 r_mcangle_other 1.109 r_angle_other_deg 0.883 r_scbond_other 0.723 r_mcbond_other 0.405 r_symmetry_vdw_other 0.219 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1387 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 96
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction