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Crystal structure of Truncated Human Coatomer Protein Complex, subunit Z1 (CopZ1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 2.2 M DL-Malic acid
0.2 M Na Malonate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.36 α = 90 b = 65.403 β = 96.58 c = 37.273 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M LN2 cooled double crystal monochromator and two horizontal deflecting and one vertical deflecting X-ray mirror 2016-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033200 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 56.03 97.3 0.046 0.998 16 3.0246 33495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 95.4 0.37 0.883 2.6 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 2HF6 1.6 56.03 31877 1619 97.34 0.21243 0.21041 0.2185 0.251 0.2635 RANDOM 20.047
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] -0.48 0.21 -0.09 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_1_deg 6.15 r_long_range_B_refined 3.529 r_long_range_B_other 3.511 r_angle_refined_deg 2.569 r_scangle_other 2.366 r_scbond_it 1.573 r_scbond_other 1.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_1_deg 6.15 r_long_range_B_refined 3.529 r_long_range_B_other 3.511 r_angle_refined_deg 2.569 r_scangle_other 2.366 r_scbond_it 1.573 r_scbond_other 1.573 r_mcangle_other 1.377 r_mcangle_it 1.376 r_angle_other_deg 1.284 r_mcbond_it 0.923 r_mcbond_other 0.913 r_chiral_restr 0.187 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing