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LSD1(KDM1A)-CoREST in complex with 1-Ethyl-Tranylcypromine
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 4.18 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.3 α = 90 b = 178.56 β = 90 c = 234.02 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 PIXEL M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3 53 99.5 0.14 7.5 3.4 49581
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 3 3.16 99.8 1.06 1.3 3.6
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 3 53.23 48610 971 99.16 0.22654 0.22615 0.2277 0.24585 0.2446 RANDOM 73.166
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] 4.22 -2.83 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.271 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_4_deg 13.669 r_dihedral_angle_1_deg 4.832 r_angle_refined_deg 0.976 r_chiral_restr 0.06 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 35.271 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_4_deg 13.669 r_dihedral_angle_1_deg 4.832 r_angle_refined_deg 0.976 r_chiral_restr 0.06 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 6293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing