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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, LITHIUM SULPHATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.297 α = 90 b = 105.887 β = 90 c = 219.52 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 CCD MARRESEARCH 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 2.2 111.8 0.252 7.4 4.6 90262 88185 28.96
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 2.2 2.32 0.852 1.9 4.6 12149
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 2.2 15 83713 4396 98.02 0.17848 0.1755 0.1861 0.23598 0.18 RANDOM 28.135
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] 0.18 0.04 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.758 r_scangle_it 4.41 r_scbond_it 2.649 r_angle_refined_deg 1.775 r_mcangle_it 1.667 r_angle_other_deg 1.113 r_mcbond_it 0.897 r_symmetry_vdw_other 0.28 r_nbd_other 0.258 r_symmetry_hbond_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.758 r_scangle_it 4.41 r_scbond_it 2.649 r_angle_refined_deg 1.775 r_mcangle_it 1.667 r_angle_other_deg 1.113 r_mcbond_it 0.897 r_symmetry_vdw_other 0.28 r_nbd_other 0.258 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.126 r_nbtor_other 0.092 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12778 Nucleic Acid Atoms Solvent Atoms 1162 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling