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Hinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPJ PDB ENTRY 1RPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 pH 9.00
Crystal Properties Matthews coefficient Solvent content 3.23 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.1 α = 90 b = 133.1 β = 90 c = 133.1 γ = 90
Symmetry Space Group P 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 3.08 29 99.5 0.0094 7.1 11.3 625
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 3.08 3.16 99.9 0.034 2.3
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 PDB ENTRY 1RPJ 3.1 29.75 7191 550 99.5 0.284 0.28 0.2509 0.339 0.3101 RANDOM 34.37
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]
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 12.191 r_mcbond_it 8.367 r_dihedral_angle_1_deg 7.037 r_scangle_it 5.941 r_scbond_it 4.338 r_angle_refined_deg 3.29 r_angle_other_deg 2.414 r_symmetry_vdw_refined 0.886 r_symmetry_vdw_other 0.628 r_chiral_restr 0.358
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 12.191 r_mcbond_it 8.367 r_dihedral_angle_1_deg 7.037 r_scangle_it 5.941 r_scbond_it 4.338 r_angle_refined_deg 3.29 r_angle_other_deg 2.414 r_symmetry_vdw_refined 0.886 r_symmetry_vdw_other 0.628 r_chiral_restr 0.358 r_symmetry_hbond_refined 0.288 r_nbd_refined 0.231 r_nbd_other 0.231 r_nbtor_other 0.122 r_xyhbond_nbd_refined 0.118 r_bond_refined_d 0.074 r_bond_other_d 0.042 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2133 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing