5CPQ

Disproportionating enzyme 1 from Arabidopsis - apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X1N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82931 microliter of 9% PEG2000 MME in 0.1 M HEPES-NaOH, pH 8.0 was added to 1 microliter of protein at a concentration of 10 mg/ml in 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.6753.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.65α = 64.97
b = 74.22β = 69.48
c = 79.7γ = 66.02
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9763DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.12670.51592.60.0840.1060.0636.72.7681856818535.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.2484.40.5410.5410.4041.42.69066

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1X1N2.1357.7864404345992.730.18840.18680.2182RANDOM42.1
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]
1.031.680.43-0.51-1.640.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_4_deg17.945
r_dihedral_angle_3_deg13.326
r_dihedral_angle_1_deg5.868
r_mcangle_it1.944
r_angle_refined_deg1.401
r_mcbond_it1.219
r_mcbond_other1.216
r_angle_other_deg0.934
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_4_deg17.945
r_dihedral_angle_3_deg13.326
r_dihedral_angle_1_deg5.868
r_mcangle_it1.944
r_angle_refined_deg1.401
r_mcbond_it1.219
r_mcbond_other1.216
r_angle_other_deg0.934
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8009
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms64

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction