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Human gamma-glutamylamine cyclotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 17.5%(w/v) PEG3350, 0.3M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.83 32.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.995 α = 90 b = 41.94 β = 90 c = 84.012 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 210 beamline optics 2009-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.956635 Australian Synchrotron MX1
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 1.2 29.68 99.9 0.058 22.2 6.8 40593 40593 -2 -2 8.717
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 1.26 99.7 0.323 5.2 6.6 5782
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 1VKB 1.2 29.68 38497 38497 2032 99.93 0.12436 0.12305 0.1231 0.14876 0.1478 RANDOM 8.889
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] -0.57 0.45 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.806 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_1_deg 6.816 r_scangle_it 5.259 r_scbond_it 4.09 r_mcangle_it 3.703 r_mcbond_it 2.932 r_rigid_bond_restr 1.918 r_angle_refined_deg 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.806 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_1_deg 6.816 r_scangle_it 5.259 r_scbond_it 4.09 r_mcangle_it 3.703 r_mcbond_it 2.932 r_rigid_bond_restr 1.918 r_angle_refined_deg 1.91 r_angle_other_deg 1.565 r_mcbond_other 1 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.008 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1192 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling