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X-ray reduced Paraccocus denitrificans methylamine dehydrogenase O- quinone in complex with amicyanin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PRE-REDUCTION O-QUINONE FORM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 pH 5.60
Crystal Properties Matthews coefficient Solvent content 3.32 62.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.733 α = 90 b = 122.733 β = 90 c = 246.591 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 2.15 21.7 99 0.11 10.3 7.8 96429 2 59.8
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 2.15 2.21 99.9 0.43 5.2 7.9
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 PRE-REDUCTION O-QUINONE FORM 2.15 21.7 96429 5081 99 0.192 0.189 0.2313 0.245 0.283 RANDOM 59.77
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 35.857 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_1_deg 8.534 r_scangle_it 4.271 r_scbond_it 3.028 r_angle_refined_deg 2.157 r_mcangle_it 1.942 r_mcbond_it 1.243 r_symmetry_vdw_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_1_deg 8.534 r_scangle_it 4.271 r_scbond_it 3.028 r_angle_refined_deg 2.157 r_mcangle_it 1.942 r_mcbond_it 1.243 r_symmetry_vdw_refined 0.341 r_nbtor_refined 0.308 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.22 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.154 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 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 9449 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling