☰ Navigation Tabs
Complex of PMM/PGM with ribose 1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 NA, K TARTRATE , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.717 α = 90 b = 74.095 β = 90 c = 84.347 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0398 APS 14-BM-C
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 2.4 50 91.7 4.2 16595
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 2.4 2.49 83.9
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT 1P5D 2.4 43.85 15600 803 91.66 0.18998 0.18998 0.18646 0.1845 0.25946 0.259 same as 1P5d 22.416
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] -0.98 -2.28 3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_4_deg 14.54 r_dihedral_angle_1_deg 5.536 r_scangle_it 1.707 r_angle_refined_deg 1.192 r_scbond_it 1.056 r_mcangle_it 0.701 r_mcbond_it 0.403 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_4_deg 14.54 r_dihedral_angle_1_deg 5.536 r_scangle_it 1.707 r_angle_refined_deg 1.192 r_scbond_it 1.056 r_mcangle_it 0.701 r_mcbond_it 0.403 r_nbtor_refined 0.3 r_nbd_refined 0.191 r_metal_ion_refined 0.183 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3430 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling