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Crystal structure of WD-repeat domain of human coatomer subunit Alpha (COPA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 3350, 0.2M di-Ammonium Tartrate
Crystal Properties Matthews coefficient Solvent content 1.83 32.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.633 α = 90 b = 85.452 β = 107.04 c = 47.913 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 RIGAKU SATURN A200 2019-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.72 50 93.6 0.088 0.096 0.037 8.3 6.4 26521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 69.3 0.472 0.532 0.236 0.833 4.1
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 4J87 1.72 20.76 25722 740 93.43 0.1727 0.1714 0.1815 0.2182 0.2283 RANDOM 17.7
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] -1.65 -0.03 1.89 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.062 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_1_deg 8.169 r_angle_refined_deg 1.352 r_angle_other_deg 1.258 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.062 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_1_deg 8.169 r_angle_refined_deg 1.352 r_angle_other_deg 1.258 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2458 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data processing