☰ Navigation Tabs
Crystal structure of NDOR1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JA1 PDB ENTRY 1JA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2 M ammonium sulfate, 0.1 M MES, 30% PEG5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.45 α = 90 b = 80.45 β = 90 c = 101.48 γ = 90
Symmetry Space Group P 43 21 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 PSI PILATUS 6M Kirkpatrick-Baez pair of bi-morph mirrors 2012-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 20.1 99.7 0.083 0.083 16.61 10.65 31433 31433 35.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 98.7 0.52 0.52 2.1 7.8 4943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1JA1 1.8 12.96 29758 29758 1566 99.35 0.21278 0.21278 0.21169 0.2155 0.23387 0.2368 RANDOM 32.275
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.964 r_dihedral_angle_3_deg 16.458 r_dihedral_angle_4_deg 15.137 r_dihedral_angle_1_deg 5.633 r_angle_refined_deg 1.285 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.964 r_dihedral_angle_3_deg 16.458 r_dihedral_angle_4_deg 15.137 r_dihedral_angle_1_deg 5.633 r_angle_refined_deg 1.285 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2442 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 62
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling