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Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphoglucomutse in an open conformation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 24-34% PEG 4000
50 mM TRIS ph 7.5
200 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.27 α = 90 b = 117.33 β = 97.78 c = 52.78 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.47 58.67 99.8 0.116 0.162 0.082 0.992 8.1 3.8 16554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.53 100 0.806 1.12 0.559 0.47 1.5 3.9
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 2WHE 2.47 58.66 15698 832 99.74 0.19723 0.19301 0.1993 0.27827 0.2744 RANDOM 41.377
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] 1.02 0.63 -0.89 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.05 r_dihedral_angle_4_deg 24.211 r_dihedral_angle_3_deg 18.291 r_long_range_B_other 7.972 r_long_range_B_refined 7.969 r_dihedral_angle_1_deg 7.028 r_scangle_other 5.957 r_mcangle_it 4.581 r_mcangle_other 4.58 r_scbond_it 3.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.05 r_dihedral_angle_4_deg 24.211 r_dihedral_angle_3_deg 18.291 r_long_range_B_other 7.972 r_long_range_B_refined 7.969 r_dihedral_angle_1_deg 7.028 r_scangle_other 5.957 r_mcangle_it 4.581 r_mcangle_other 4.58 r_scbond_it 3.906 r_scbond_other 3.886 r_mcbond_other 3.087 r_mcbond_it 3.086 r_angle_refined_deg 1.62 r_angle_other_deg 1.244 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3378 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing