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LSD1-tranylcypromine complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DW4 PDB ENTRY 2DW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 3.5-4% PEG 2000, 0.1M HEPES-Na, 5% MPD, 5mM Tranylcypromine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 3.68 66.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.759 α = 90 b = 185.759 β = 90 c = 108.742 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315 mirrors 2006-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 48.1 99 0.133 25.7 19.7 30564 -3 66.8
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) 2.7 2.8 91.4 0.687 2.1 11.2 2765
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 PDB ENTRY 2DW4 2.7 48.1 30523 1527 98.9 0.2042 0.2042 0.2051 0.2447 0.201 RANDOM 49.3
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] 5.88 11.18 5.88 -11.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 7.58 c_scbond_it 5.64 c_mcangle_it 5.01 c_mcbond_it 3.37 c_angle_deg 1.4 c_improper_angle_d 1.12 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 7.58 c_scbond_it 5.64 c_mcangle_it 5.01 c_mcbond_it 3.37 c_angle_deg 1.4 c_improper_angle_d 1.12 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5052 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 63
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing