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X-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E. coli Maltodextrin Phosphorylase (MalP)
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 PEG 4000, lithium chloride, (hydroxymethyl) aminomethane, maltopentaose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.3 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.327 α = 90 b = 104.723 β = 90 c = 214.787 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 mirrors 2004-03-31 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 1.95 15 97.8 0.119 10.1 3.9 121744 119849 25.9
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 1.95 2.06 91.1 0.476 1.8 2.7 16075
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 1.95 15 113766 6018 97.46 0.18168 0.17939 0.191 0.22604 0.1872 RANDOM 30.275
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] -0.8 -1 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.442 r_scangle_it 4.099 r_angle_other_deg 3.679 r_scbond_it 2.534 r_angle_refined_deg 1.633 r_mcangle_it 1.568 r_mcbond_it 0.88 r_symmetry_vdw_other 0.325 r_nbd_other 0.286 r_symmetry_vdw_refined 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.442 r_scangle_it 4.099 r_angle_other_deg 3.679 r_scbond_it 2.534 r_angle_refined_deg 1.633 r_mcangle_it 1.568 r_mcbond_it 0.88 r_symmetry_vdw_other 0.325 r_nbd_other 0.286 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.164 r_nbtor_other 0.11 r_chiral_restr 0.105 r_bond_refined_d 0.019 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 1184 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement MAR345 data collection CCP4 data scaling