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crystal structure of cofactor(NAD+) bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 25% PEG 3350, 100mM Tris pH 7.0-8.0 300mM sodium formate, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.378 α = 66.71 b = 56.857 β = 66.22 c = 57.259 γ = 77.36
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 IMAGE PLATE RIGAKU RAXIS IV++ 2012-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.22 52.09 95.6 24702 -3
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 2.22 2.3 90.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.22 52.09 23444 1257 95.48 0.20343 0.20114 0.2012 0.24604 0.2457 RANDOM 45.223
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] -2.64 -2.25 2.03 4.36 -1.84 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_4_deg 12.31 r_dihedral_angle_1_deg 5.01 r_mcangle_it 1.621 r_mcbond_other 1.322 r_scbond_it 1.056 r_mcbond_it 0.934 r_angle_refined_deg 0.918 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_4_deg 12.31 r_dihedral_angle_1_deg 5.01 r_mcangle_it 1.621 r_mcbond_other 1.322 r_scbond_it 1.056 r_mcbond_it 0.934 r_angle_refined_deg 0.918 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg 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_mcangle_other r_scbond_other r_scangle_it 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 4724 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing