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X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L5V PDB ENTRY 1L5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 PEG4000, Lithium chloride, TRIS (hydroxymethil) aminomethane, maltopentaose, alluminium nitrate, sodium fluoride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.957 α = 90 b = 105.614 β = 90 c = 218.629 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 IMAGE PLATE MARRESEARCH MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.01 111.8 0.149 6.7 2.1 102161 100613 21.8
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 2.01 2.11 0.447 2 1.9 10682
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 PDB ENTRY 1L5V 2.01 15 95530 5058 86.29 0.1927 0.18998 0.2002 0.24387 0.194 RANDOM 24.683
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] -0.97 -1.15 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.59 r_scangle_it 3.898 r_angle_other_deg 3.762 r_scbond_it 2.407 r_angle_refined_deg 1.667 r_mcangle_it 1.501 r_mcbond_it 0.85 r_symmetry_vdw_other 0.327 r_nbd_other 0.281 r_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.59 r_scangle_it 3.898 r_angle_other_deg 3.762 r_scbond_it 2.407 r_angle_refined_deg 1.667 r_mcangle_it 1.501 r_mcbond_it 0.85 r_symmetry_vdw_other 0.327 r_nbd_other 0.281 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.164 r_nbtor_other 0.109 r_chiral_restr 0.107 r_bond_refined_d 0.02 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12778 Nucleic Acid Atoms Solvent Atoms 1145 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling