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Human gamma-glutamylamine cyclotransferase complex with 5-oxoproline
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 22.5%(w/v) PEG3350, 0.2M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.88 34.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.247 α = 90 b = 42.478 β = 90 c = 84.814 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 210r beamline optics 2009-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954448 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 42.52 98.5 0.055 27.5 9 40928 40928 -2 -2 8.701
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 97 0.154 10.7 6.9 5805
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VKB 1.2 42.41 38832 38832 2053 98.23 0.1187 0.1187 0.11711 0.14757 0.1697 RANDOM 9.783
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] -0.56 0.21 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.229 r_dihedral_angle_4_deg 18.632 r_dihedral_angle_3_deg 11.884 r_dihedral_angle_1_deg 7.962 r_scangle_it 5.567 r_scbond_it 4.3 r_mcangle_it 4.157 r_mcbond_it 3.083 r_rigid_bond_restr 2.147 r_angle_refined_deg 1.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.229 r_dihedral_angle_4_deg 18.632 r_dihedral_angle_3_deg 11.884 r_dihedral_angle_1_deg 7.962 r_scangle_it 5.567 r_scbond_it 4.3 r_mcangle_it 4.157 r_mcbond_it 3.083 r_rigid_bond_restr 2.147 r_angle_refined_deg 1.922 r_mcbond_other 1.108 r_angle_other_deg 0.966 r_chiral_restr 0.11 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 1271 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 17
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling