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Crystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase in complex with N-acetylhistamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 30%(v/v) PEG 200, 5%(w/v) PEG 3000, 0.1M Mes, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.91 35.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.301 α = 90 b = 68.58 β = 90 c = 77.439 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2010-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 1.13 30 98.7 0.063 62.1 13.1 106645 105259 3 3
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 1.13 1.17 92.2 0.292 4.4 7.4 10510
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3PB4 1.13 30 101329 99921 5244 98.61 0.13252 0.13102 0.1564 0.16107 0.1554 RANDOM 15.604
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] 0.95 -0.44 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_4_deg 23.304 r_dihedral_angle_3_deg 11.97 r_scangle_it 6.216 r_dihedral_angle_1_deg 6.056 r_scbond_it 4.493 r_mcangle_it 3.135 r_rigid_bond_restr 2.66 r_mcbond_it 2.185 r_angle_refined_deg 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_4_deg 23.304 r_dihedral_angle_3_deg 11.97 r_scangle_it 6.216 r_dihedral_angle_1_deg 6.056 r_scbond_it 4.493 r_mcangle_it 3.135 r_rigid_bond_restr 2.66 r_mcbond_it 2.185 r_angle_refined_deg 2.156 r_chiral_restr 0.123 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2474 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling