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Complex of glucose-1,6-bisphosphate with phosphomannomutase from Leishmania mexicana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 14% (w/v) PEG 3350, 10% PEG 400, 0.1M citrate, 50% PEG 3550, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.224 α = 90 b = 92.224 β = 90 c = 172.824 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
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 2.9 50 90.6 0.065 17.3 3.6 17996
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 2.9 3 84.5 0.311 3.4 1645
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2I54 2.9 46.7 17862 912 100 0.195 0.192 0.1861 0.268 0.2649 RANDOM 60.431
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] -2.31 -1.15 -2.31 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.138 r_dihedral_angle_3_deg 17.965 r_dihedral_angle_4_deg 13.264 r_dihedral_angle_1_deg 6.663 r_angle_refined_deg 1.371 r_scangle_it 1.315 r_scbond_it 0.843 r_angle_other_deg 0.755 r_mcangle_it 0.503 r_mcbond_it 0.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.138 r_dihedral_angle_3_deg 17.965 r_dihedral_angle_4_deg 13.264 r_dihedral_angle_1_deg 6.663 r_angle_refined_deg 1.371 r_scangle_it 1.315 r_scbond_it 0.843 r_angle_other_deg 0.755 r_mcangle_it 0.503 r_mcbond_it 0.404 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.222 r_symmetry_vdw_other 0.205 r_nbtor_refined 0.192 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.145 r_nbtor_other 0.087 r_chiral_restr 0.067 r_mcbond_other 0.061 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5838 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction