☰ Navigation Tabs
Crystal structure of the human anterior gradient protein 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295.15 25 % PEG 4000, 0.2 M MgCl2, 0.2 M NaCl, 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 1.97 37.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.29 α = 90 b = 71.45 β = 97.72 c = 59.81 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.83 50 99 0.108 15.5 7.5 24330 22.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1SEN 1.83 45.62 24330 23102 1228 99.06 0.17968 0.17697 0.2326 0.2216 RANDOM 15.492
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] -0.33 0.43 0.23 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.022 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_4_deg 12.878 r_dihedral_angle_1_deg 6.116 r_scangle_it 3.53 r_scbond_it 2.178 r_angle_refined_deg 1.396 r_mcangle_it 1.333 r_angle_other_deg 0.915 r_mcbond_it 0.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.022 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_4_deg 12.878 r_dihedral_angle_1_deg 6.116 r_scangle_it 3.53 r_scbond_it 2.178 r_angle_refined_deg 1.396 r_mcangle_it 1.333 r_angle_other_deg 0.915 r_mcbond_it 0.739 r_mcbond_other 0.194 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2207 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling