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Structure of non-fluorescent human amniotic fluid RBP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4.3 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.54 65.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.58 α = 90 b = 102.58 β = 90 c = 73.282 γ = 120
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 2016-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0 ESRF ID29
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 1.68 56.53 95.3 0.067 7.8 2.5 31219
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 1.68 1.77 93.7 0.45 2 2.4
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 FOURIER SYNTHESIS THROUGHOUT 5NTY 1.68 30 29609 1602 95.27 0.17089 0.16949 0.2177 0.19711 0.2212 RANDOM 42.121
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] 0.98 0.49 0.98 -3.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_sphericity_bonded 25.984 r_sphericity_free 22.175 r_dihedral_angle_4_deg 14.253 r_dihedral_angle_3_deg 13.394 r_rigid_bond_restr 12.412 r_scangle_other 11.892 r_scbond_it 11.819 r_scbond_other 11.812 r_long_range_B_other 11.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_sphericity_bonded 25.984 r_sphericity_free 22.175 r_dihedral_angle_4_deg 14.253 r_dihedral_angle_3_deg 13.394 r_rigid_bond_restr 12.412 r_scangle_other 11.892 r_scbond_it 11.819 r_scbond_other 11.812 r_long_range_B_other 11.474 r_long_range_B_refined 11.38 r_mcangle_it 8.821 r_mcangle_other 8.744 r_dihedral_angle_1_deg 8.207 r_mcbond_other 8.179 r_mcbond_it 8.111 r_angle_other_deg 1.118 r_angle_refined_deg 0.684 r_chiral_restr 0.037 r_bond_other_d 0.006 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1408 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling