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Crystal structure of FAP in the dark at 100K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 281 PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.69 α = 90 b = 103.57 β = 90 c = 155.95 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS EIGER X 4M 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97372 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.78 86 99.3 0.086 0.096 0.998 11.02 4.727 69240 34.226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.9 99.4 1.132 1.269 0.512 1.03 4.838
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NCC 1.78 46.503 69195 3431 99.213 0.174 0.1721 0.1815 0.2021 0.2127 30.186
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] 0.73 0.486 -1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.381 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 12.788 r_lrange_it 10.061 r_lrange_other 9.773 r_dihedral_angle_1_deg 7.482 r_scangle_it 6.17 r_scangle_other 6.169 r_scbond_other 4.613 r_scbond_it 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.381 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 12.788 r_lrange_it 10.061 r_lrange_other 9.773 r_dihedral_angle_1_deg 7.482 r_scangle_it 6.17 r_scangle_other 6.169 r_scbond_other 4.613 r_scbond_it 4.61 r_mcangle_other 3.218 r_mcangle_it 3.216 r_mcbond_it 2.346 r_mcbond_other 2.339 r_angle_refined_deg 1.661 r_angle_other_deg 1.468 r_symmetry_nbd_refined 0.278 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.235 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4267 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction