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Structure of the P368G mutant of PMM/PGM in complex with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5G PDB entry 1P5G
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 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.604 α = 90 b = 74.74 β = 90 c = 86.924 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 NOIR-1 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
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 2.05 44.2 99.6 0.132 7.2 6.69 29408
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 2.05 2.12 99.2 0.491 3.1 6.4
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 refinement THROUGHOUT PDB entry 1P5G 2.05 44.2 27873 1492 99.43 0.21955 0.21792 0.218 0.24931 0.2483 RANDOM 29.539
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] -1.45 -1.13 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.985 r_dihedral_angle_4_deg 20.621 r_dihedral_angle_3_deg 16.045 r_dihedral_angle_1_deg 6.042 r_scangle_it 2.576 r_scbond_it 1.657 r_angle_refined_deg 1.418 r_mcangle_it 0.985 r_mcbond_it 0.609 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.985 r_dihedral_angle_4_deg 20.621 r_dihedral_angle_3_deg 16.045 r_dihedral_angle_1_deg 6.042 r_scangle_it 2.576 r_scbond_it 1.657 r_angle_refined_deg 1.418 r_mcangle_it 0.985 r_mcbond_it 0.609 r_nbtor_refined 0.304 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.159 r_metal_ion_refined 0.127 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 3448 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling