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Crystal structure of GLTP with bound GM3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TFJ PDB ENTRY 1TFJ
Crystallization Crystal Properties Matthews coefficient Solvent content 2.1 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.5 α = 90 b = 34.6 β = 116.5 c = 58.3 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 ADSC CCD 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 25 99.5 0.08 16.6 6 115280 -3
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 1.8 1.9 99.7 0.52 4.2 6.14
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 1TFJ 1.79 52.2 17930 974 99.4 0.193 0.189 0.1889 0.257 0.2568 RANDOM 22.82
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] -0.64 0.58 0.04 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 5.48 r_scangle_it 3.384 r_scbond_it 2.135 r_mcangle_it 1.493 r_angle_refined_deg 1.359 r_mcbond_it 0.994 r_symmetry_vdw_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 5.48 r_scangle_it 3.384 r_scbond_it 2.135 r_mcangle_it 1.493 r_angle_refined_deg 1.359 r_mcbond_it 0.994 r_symmetry_vdw_refined 0.331 r_nbtor_refined 0.317 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.091 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1633 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOLREP phasing