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Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 16% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.59 α = 90 b = 97.47 β = 97.66 c = 105.27 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 CCD MARMOSAIC 225 mm CCD 2014-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 1.4 35 98.7 0.074 10.7 5.3 398539
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 1.4 1.42 97.3 0.542 3 5.3
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 4ZE5 1.4 22.37 373525 19771 98.7 0.132 0.13 0.1306 0.158 0.1582 RANDOM 14.27
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] -0.53 0.04 0.65 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 7.202 r_long_range_B_other 7.201 r_scangle_other 4.363 r_scbond_it 2.976 r_scbond_other 2.976 r_angle_refined_deg 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 7.202 r_long_range_B_other 7.201 r_scangle_other 4.363 r_scbond_it 2.976 r_scbond_other 2.976 r_angle_refined_deg 2.67 r_mcangle_other 2.573 r_mcangle_it 2.572 r_mcbond_it 1.726 r_mcbond_other 1.718 r_angle_other_deg 1.081 r_chiral_restr 0.159 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 r_bond_other_d 0.002 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 15140 Nucleic Acid Atoms Solvent Atoms 2578 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing