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Crystal structure of human monoamine oxidase B in complex with styrylpiperidine analogue 97
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG 4000, lithium sulphate, ADA buffer
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.818 α = 90 b = 223.453 β = 90 c = 86.557 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2017-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.98 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.3 47.66 95.7 0.12 0.99 8.6 4 54756
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37
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 2v5z 2.3 47.66 53334 1419 95.1 0.18875 0.18723 0.1939 0.24475 0.2507 RANDOM 39.257
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] 3.38 -1.27 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 16.573 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.788 r_long_range_B_refined 6.428 r_long_range_B_other 6.427 r_scangle_other 4.98 r_mcangle_it 3.669 r_mcangle_other 3.669 r_scbond_it 3.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 16.573 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.788 r_long_range_B_refined 6.428 r_long_range_B_other 6.427 r_scangle_other 4.98 r_mcangle_it 3.669 r_mcangle_other 3.669 r_scbond_it 3.199 r_scbond_other 3.198 r_mcbond_it 2.458 r_mcbond_other 2.453 r_angle_other_deg 1.472 r_angle_refined_deg 1.317 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7914 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing