☰ Navigation Tabs
Crystal structure of human 3-phosphoglycerate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YGY PDB ENTRY 1YGY, 1PSD experimental model PDB 1PSD PDB ENTRY 1YGY, 1PSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M MMT, 30 % PEG1k, 5mM NAD+, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.084 α = 90 b = 124.113 β = 100.99 c = 59.502 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 MARMOSAIC 225 mm CCD 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99806 SLS X10SA
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 1.7 36.2 98.9 66626 66626
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 1.7 1.76 96.1
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 PDB ENTRY 1YGY, 1PSD 1.7 36.2 63219 63219 3371 98.6 0.1828 0.18098 0.1872 0.21644 0.2196 RANDOM 25.461
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] 0.12 -0.08 2 -2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_3_deg 12.983 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 5.893 r_scangle_it 2.637 r_scbond_it 1.759 r_angle_refined_deg 1.453 r_mcangle_it 1.014 r_angle_other_deg 0.932 r_mcbond_it 0.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_3_deg 12.983 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 5.893 r_scangle_it 2.637 r_scbond_it 1.759 r_angle_refined_deg 1.453 r_mcangle_it 1.014 r_angle_other_deg 0.932 r_mcbond_it 0.709 r_nbd_refined 0.221 r_nbd_other 0.199 r_symmetry_vdw_other 0.194 r_mcbond_other 0.186 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.129 r_nbtor_other 0.085 r_chiral_restr 0.081 r_symmetry_vdw_refined 0.046 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4413 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing