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X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 pH 9.00
Crystal Properties Matthews coefficient Solvent content 3.31 62.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.029 α = 90 b = 123.029 β = 90 c = 245.303 γ = 90
Symmetry Space Group P 41 21 2
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 APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.1 43.5 97.4 0.13 22 9.7 101798 2 29.3
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 2.1 2.18 100 0.5 7.8 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT 2.1 43.48 101798 5353 97.4 0.171 0.169 0.207 0.2167 RANDOM 29.32
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 15.713 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 8.954 r_scangle_it 3.836 r_scbond_it 2.411 r_angle_refined_deg 1.637 r_mcangle_it 1.474 r_mcbond_it 0.849 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 15.713 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 8.954 r_scangle_it 3.836 r_scbond_it 2.411 r_angle_refined_deg 1.637 r_mcangle_it 1.474 r_mcbond_it 0.849 r_nbtor_refined 0.31 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 9342 Nucleic Acid Atoms Solvent Atoms 1033 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling