☰ Navigation Tabs
Structure of GAPDH with CP12 peptide from Thermosynechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZCX PDB ENTRY 3ZCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BICINE PH 9, 10 % W/V PEG 20,000/ 2% V/V DIOXANE
Crystal Properties Matthews coefficient Solvent content 2.47 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.45 α = 90 b = 141.45 β = 90 c = 77.39 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 DECTRIS PILATUS 6M 2012-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.34 63.26 99.9 0.14 5.38 6.61 33680
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 2.34 2.4 99.9 0.65 1.18 6.53
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 3ZCX 2.34 63.26 31926 1703 99.87 0.17539 0.17331 0.1797 0.21464 0.2189 RANDOM 29.036
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] -0.25 -0.25 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.428 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_1_deg 6.722 r_long_range_B_refined 4.422 r_long_range_B_other 4.409 r_scangle_other 2.588 r_mcangle_it 2.162 r_mcangle_other 2.162 r_angle_refined_deg 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.428 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_1_deg 6.722 r_long_range_B_refined 4.422 r_long_range_B_other 4.409 r_scangle_other 2.588 r_mcangle_it 2.162 r_mcangle_other 2.162 r_angle_refined_deg 1.746 r_scbond_it 1.578 r_scbond_other 1.578 r_mcbond_it 1.286 r_mcbond_other 1.286 r_angle_other_deg 1.029 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5517 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing