☰ Navigation Tabs
Structure of Helix Pomatia agglutinin with no ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCV PDB ENTRY 2CCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5).
Crystal Properties Matthews coefficient Solvent content 2.53 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.6 α = 90 b = 61.6 β = 90 c = 105 γ = 120
Symmetry Space Group P 63 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 CCD ADSC CCD MIRROR 2002-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.4 52.49 99.8 0.07 22.67 7.35 5042 56
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 2.4 2.43 99.8 0.38 2.59 4.37
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 2CCV 2.4 47.57 4785 236 99.6 0.224 0.222 0.2225 0.266 0.281 RANDOM 52.99
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] -2.02 -1.01 -2.02 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.573 r_dihedral_angle_4_deg 23.151 r_dihedral_angle_3_deg 15.467 r_dihedral_angle_1_deg 5.9 r_scangle_it 2.058 r_angle_refined_deg 1.458 r_scbond_it 1.335 r_mcangle_it 0.991 r_mcbond_it 0.804 r_angle_other_deg 0.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.573 r_dihedral_angle_4_deg 23.151 r_dihedral_angle_3_deg 15.467 r_dihedral_angle_1_deg 5.9 r_scangle_it 2.058 r_angle_refined_deg 1.458 r_scbond_it 1.335 r_mcangle_it 0.991 r_mcbond_it 0.804 r_angle_other_deg 0.787 r_symmetry_vdw_other 0.205 r_nbd_other 0.196 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.168 r_nbtor_other 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 780 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing