☰ Navigation Tabs
Histone demethylase LSD1(KDM1A)-CoREST3 Complex
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 3.95 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.04 α = 90 b = 177.44 β = 90 c = 235.79 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 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 3 70.89 99.8 0.19 6.5 5.1 49662
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 3.1 100 0.82 1.3 5.3
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 3 141.78 48573 971 99.33 0.1973 0.1965 0.2066 0.23612 0.239 RANDOM 79.98
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] 10.36 -6.76 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 23.029 r_dihedral_angle_3_deg 20.976 r_mcangle_it 9.219 r_dihedral_angle_1_deg 6.562 r_scbond_it 6.518 r_mcbond_it 6.049 r_mcbond_other 6.049 r_angle_refined_deg 1.731 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 23.029 r_dihedral_angle_3_deg 20.976 r_mcangle_it 9.219 r_dihedral_angle_1_deg 6.562 r_scbond_it 6.518 r_mcbond_it 6.049 r_mcbond_other 6.049 r_angle_refined_deg 1.731 r_angle_other_deg 0.863 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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_mcangle_other 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 6286 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing