1VKP

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729710 mg/ml protein, 18% PEG 4000, 8% ethylene glycol, 100 mM MOPS, Vapor diffusion, hanging drop, pH 7.00, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.5551.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 115.813β = 97.1
c = 66.634γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmRH MIRROR2004-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-IDAPS32-ID

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
11.532598.20.09111.697.9127993
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)
1.531.5896.30.3223.236.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5319.8811392060381000.1480.1460.174RANDOM17.43
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.336
r_scangle_it5.799
r_scbond_it3.813
r_mcangle_it2.676
r_angle_refined_deg1.556
r_mcbond_it1.545
r_angle_other_deg0.915
r_mcbond_other0.307
r_symmetry_vdw_other0.306
r_nbd_other0.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.336
r_scangle_it5.799
r_scbond_it3.813
r_mcangle_it2.676
r_angle_refined_deg1.556
r_mcbond_it1.545
r_angle_other_deg0.915
r_mcbond_other0.307
r_symmetry_vdw_other0.306
r_nbd_other0.258
r_nbd_refined0.217
r_nbtor_refined0.18
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.162
r_chiral_restr0.097
r_nbtor_other0.084
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.01
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5853
Nucleic Acid Atoms
Solvent Atoms779
Heterogen Atoms67

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ARP/wARPmodel building