3JUD | pdb_00003jud

Human gamma-glutamylamine cyclotransferase, E82Q mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729812.5%(w/v) PEG3350, 0.3M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.8834.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.307α = 90
b = 42.443β = 90
c = 84.764γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rbeamline optics2009-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.826966Australian SynchrotronMX2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.9837.9597.70.1040.10410.46.77420074200-2-25
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)RedundancyNumber Unique Reflections (All)
0.981.031000.6880.6882.56.810958

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VKB0.9827.577035770357373697.540.154780.153490.160.179690.19RANDOM8.444
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]
-0.080.1-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.515
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg12.716
r_dihedral_angle_1_deg6.976
r_scangle_it6.032
r_scbond_it4.396
r_mcangle_it3.549
r_mcbond_it2.603
r_angle_refined_deg2.313
r_rigid_bond_restr1.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.515
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg12.716
r_dihedral_angle_1_deg6.976
r_scangle_it6.032
r_scbond_it4.396
r_mcangle_it3.549
r_mcbond_it2.603
r_angle_refined_deg2.313
r_rigid_bond_restr1.997
r_angle_other_deg1.149
r_mcbond_other0.924
r_chiral_restr0.153
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms1206
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms12

Software

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