3JUC | pdb_00003juc

Human gamma-glutamylamine cyclotransferase complex with 5-oxoproline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VKB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729822.5%(w/v) PEG3350, 0.2M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.8834.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.247α = 90
b = 42.478β = 90
c = 84.814γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rbeamline optics2009-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.954448Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.242.5298.50.05527.594092840928-2-28.701
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.26970.15410.76.95805

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VKB1.242.413883238832205398.230.11870.11870.117110.120.147570.15RANDOM9.783
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]
-0.560.210.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.229
r_dihedral_angle_4_deg18.632
r_dihedral_angle_3_deg11.884
r_dihedral_angle_1_deg7.962
r_scangle_it5.567
r_scbond_it4.3
r_mcangle_it4.157
r_mcbond_it3.083
r_rigid_bond_restr2.147
r_angle_refined_deg1.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.229
r_dihedral_angle_4_deg18.632
r_dihedral_angle_3_deg11.884
r_dihedral_angle_1_deg7.962
r_scangle_it5.567
r_scbond_it4.3
r_mcangle_it4.157
r_mcbond_it3.083
r_rigid_bond_restr2.147
r_angle_refined_deg1.922
r_mcbond_other1.108
r_angle_other_deg0.966
r_chiral_restr0.11
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1271
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms17

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling