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Human carboxypeptidase A4 in complex with human latexin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CPA4 WITHIN PCPA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 40% MPD; 0.1M BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.922 α = 90 b = 96.651 β = 99.6 c = 92.358 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.6 48.3 99.8 0.07 11.8 3.8 179401 13.5
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 1.6 1.69 99.3 0.26 4.8 3.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT CPA4 WITHIN PCPA4 1.6 50 178706 678 99.8 0.15 0.149 0.176 RANDOM 17.28
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] 1.98 -0.24 -1.36 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 6.187 r_scangle_it 3.357 r_scbond_it 2.126 r_angle_refined_deg 1.348 r_mcangle_it 1.343 r_mcbond_it 0.884 r_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 6.187 r_scangle_it 3.357 r_scbond_it 2.126 r_angle_refined_deg 1.348 r_mcangle_it 1.343 r_mcbond_it 0.884 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8404 Nucleic Acid Atoms Solvent Atoms 1153 Heterogen Atoms 146
Software Software Software Name Purpose DM model building SCALA data scaling AMoRE phasing MLPHARE phasing SIGMAA phasing DM phasing REFMAC refinement