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LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1S,2R)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1D PDB ENTRY 2V1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.25 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.16 α = 90 b = 180.04 β = 90 c = 234.58 γ = 90
Symmetry Space Group I 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 PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.8 60 99.9 0.09 9.3 4 62197
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 2.8 2.95 99.8 0.54 2.5 4
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 2V1D 2.8 50 60996 1197 99.77 0.22188 0.22159 0.2197 0.23558 0.2326 RANDOM 83.932
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] 4.57 -3.32 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 13.07 r_dihedral_angle_1_deg 4.256 r_angle_refined_deg 0.888 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 13.07 r_dihedral_angle_1_deg 4.256 r_angle_refined_deg 0.888 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6292 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing