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Crystal Structure of the Glutaminyl Cyclase from Xanthomonas campestris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAW PDB ENTRY 2FAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.68 298 50mM imidazole, 0.8M sodium citrate, pH 8.68, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.33 α = 90 b = 95.33 β = 90 c = 65.088 γ = 90
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 mirrors 2009-06-18 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 315
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.44 30 99.9 0.034 0.034 55.1 6.3 52562 52509 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.49 100 0.454 0.454 3.2 4.4 5208
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 PDB ENTRY 2FAW 1.44 29.31 49906 49776 2669 99.74 0.17625 0.17447 0.1998 0.20871 0.2088 RANDOM 32.138
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.798 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 13.728 r_sphericity_free 8.931 r_scangle_it 7.385 r_dihedral_angle_1_deg 7.068 r_sphericity_bonded 7.019 r_scbond_it 5.185 r_mcangle_it 4.103 r_rigid_bond_restr 3.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.798 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 13.728 r_sphericity_free 8.931 r_scangle_it 7.385 r_dihedral_angle_1_deg 7.068 r_sphericity_bonded 7.019 r_scbond_it 5.185 r_mcangle_it 4.103 r_rigid_bond_restr 3.311 r_mcbond_it 2.863 r_angle_refined_deg 2.301 r_chiral_restr 0.184 r_bond_refined_d 0.027 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1881 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing