☰ Navigation Tabs
Crystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 294 30% (v/v) P550MME/P20K, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.391 α = 77.62 b = 72.115 β = 79.58 c = 101.714 γ = 75.63
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 210r 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 Australian Synchrotron MX1
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 2.2 46.68 98.3 78703
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 2.2 2.25 95.8 0.827 1.9 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CE9 2.2 46.68 80009 74699 4013 98.3 0.185 0.185 0.1922 0.225 0.227 RANDOM 34.53
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] -0.81 0.74 0.42 2.35 1.18 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.513 r_long_range_B_refined 5.904 r_long_range_B_other 5.904 r_dihedral_angle_1_deg 5.141 r_scangle_other 4.535 r_mcangle_it 3.666 r_mcangle_other 3.666 r_scbond_it 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.513 r_long_range_B_refined 5.904 r_long_range_B_other 5.904 r_dihedral_angle_1_deg 5.141 r_scangle_other 4.535 r_mcangle_it 3.666 r_mcangle_other 3.666 r_scbond_it 2.914 r_scbond_other 2.914 r_angle_other_deg 2.726 r_mcbond_it 2.484 r_mcbond_other 2.483 r_angle_refined_deg 1.577 r_chiral_restr 0.089 r_gen_planes_other 0.022 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 10348 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 261
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling