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Gamma-glutamyl cyclotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.25 277.15 0.1M potassium acetate buffer pH 4.25, 20% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.07 40.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.926 α = 90 b = 99.406 β = 90 c = 99.948 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.1 20 78.8 0.083 10.04 2.2 16603 16603 -2 -2 20.665
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 2.1 2.17 78 0.268 3.93 2.1 1613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2PN7 2.1 14.97 -1 -1 15717 15717 865 78.7 0.20326 0.20326 0.20056 0.2039 0.25469 0.2577 RANDOM 26.321
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] -0.51 0.6 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_4_deg 9.811 r_dihedral_angle_1_deg 5.49 r_scangle_it 5.44 r_scbond_it 3.633 r_mcangle_it 2.461 r_mcbond_it 1.58 r_angle_refined_deg 1.231 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_4_deg 9.811 r_dihedral_angle_1_deg 5.49 r_scangle_it 5.44 r_scbond_it 3.633 r_mcangle_it 2.461 r_mcbond_it 1.58 r_angle_refined_deg 1.231 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2673 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling