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Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 20 mM glutamic acid (racemic), 20 mM glycine, 20 mM serine (racemic), 20 mM alanine (racemic), 20 mM lysine-HCl (racemic), 50 mM MOPS, 50 mM Sodium HEPES, pH 7.5; 20% Ethylene Glycol, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.289 α = 90 b = 152.353 β = 92.19 c = 149.905 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 PIXEL DECTRIS PILATUS 6M 2015-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.95 48.1 99.8 0.092 0.999 14.38 6.84 310836 37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 98.9 1.98
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 3K2W 2.05 48.1 253577 13347 99.94 0.17021 0.16838 0.1769 0.2054 0.2097 RANDOM 37.134
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] 2.47 -1.04 -2.5 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.763 r_dihedral_angle_4_deg 19.735 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 6.314 r_long_range_B_refined 6.092 r_long_range_B_other 6.061 r_angle_refined_deg 1.748 r_scangle_other 1.163 r_angle_other_deg 1.03 r_mcangle_it 0.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.763 r_dihedral_angle_4_deg 19.735 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 6.314 r_long_range_B_refined 6.092 r_long_range_B_other 6.061 r_angle_refined_deg 1.748 r_scangle_other 1.163 r_angle_other_deg 1.03 r_mcangle_it 0.753 r_mcangle_other 0.753 r_scbond_it 0.73 r_scbond_other 0.722 r_mcbond_it 0.439 r_mcbond_other 0.439 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 30004 Nucleic Acid Atoms Solvent Atoms 1353 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement XDS data reduction BALBES phasing XDS data scaling