☰ Navigation Tabs
The Crystal Structure of the Human IRp60 Ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.49 α = 90 b = 61.24 β = 90 c = 106.19 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARMOSAIC 225 mm CCD Pt coated mirrors 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 22.8 100
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 1.7 22.8
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 2NMS 1.7 22.8 36938 1859 97.7 0.218 0.215 0.2143 0.274 0.2735 RANDOM 27.038
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] 0.37 -0.4 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 25.179 r_dihedral_angle_3_deg 16.411 r_dihedral_angle_1_deg 9.492 r_sphericity_free 7.847 r_scangle_it 4.877 r_scbond_it 4.036 r_rigid_bond_restr 3.893 r_sphericity_bonded 3.658 r_mcangle_it 2.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 25.179 r_dihedral_angle_3_deg 16.411 r_dihedral_angle_1_deg 9.492 r_sphericity_free 7.847 r_scangle_it 4.877 r_scbond_it 4.036 r_rigid_bond_restr 3.893 r_sphericity_bonded 3.658 r_mcangle_it 2.254 r_angle_refined_deg 1.862 r_mcbond_it 1.465 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2507 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction BALBES phasing