2A33

X-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabidopsis Thaliana Gene AT2G37210


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDHPDB ENTRY 1YDH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529610 MG/ML PROTEIN, 22% PEG 2K, 0.084 M MAGNESIUM SULFATE, 0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 296K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
1.934

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.403α = 90
b = 66.773β = 90
c = 98.639γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-BM

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
11.955099.80.115.00910.726424
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)
1.952.0298.60.5181.7564.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YDH1.9546.98425025133699.80.1830.1810.234RANDOM29.22
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]
-0.34-0.310.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.466
r_dihedral_angle_4_deg19.02
r_dihedral_angle_3_deg15.764
r_scangle_it7.146
r_dihedral_angle_1_deg6.324
r_scbond_it5.342
r_mcangle_it2.946
r_mcbond_it1.861
r_angle_refined_deg1.712
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.466
r_dihedral_angle_4_deg19.02
r_dihedral_angle_3_deg15.764
r_scangle_it7.146
r_dihedral_angle_1_deg6.324
r_scbond_it5.342
r_mcangle_it2.946
r_mcbond_it1.861
r_angle_refined_deg1.712
r_nbtor_refined0.304
r_symmetry_vdw_refined0.271
r_nbd_refined0.212
r_xyhbond_nbd_refined0.175
r_chiral_restr0.135
r_symmetry_hbond_refined0.126
r_metal_ion_refined0.026
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2636
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms11

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction