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Crystal structure of mouse APCDD1 in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8E0P PDB entry 8E0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.861 α = 90 b = 144.128 β = 99.52 c = 64.381 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 PIXEL DECTRIS EIGER X 16M 2019-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.92009 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.947 34.364 91.1 0.135 0.057 0.996 8.5 6.3 49930
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.947 2.12 1.464 0.58 0.56 1.3
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 8E0P 1.95 34 47515 2405 76.64 0.2111 0.2092 0.2641 0.2471 0.294 RANDOM 9.798
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] -0.15 -0.12 -0.01 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.206 r_dihedral_angle_4_deg 17.829 r_dihedral_angle_3_deg 16.498 r_dihedral_angle_1_deg 7.54 r_angle_refined_deg 1.405 r_angle_other_deg 1.191 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.206 r_dihedral_angle_4_deg 17.829 r_dihedral_angle_3_deg 16.498 r_dihedral_angle_1_deg 7.54 r_angle_refined_deg 1.405 r_angle_other_deg 1.191 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6656 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 70
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction STARANISO data scaling