1PJ7

Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PJ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529415% PEG 2000MME, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.6252.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.621α = 90
b = 223.74β = 90
c = 119.371γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.9EMBL/DESY, HAMBURGX11

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
12.12088.30.0736.22.54656446564
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1584.5

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1PJ62.120465644656424821000.162530.162530.159340.22172RANDOM33.336
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]
-1.02-0.571.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.771
r_dihedral_angle_1_deg6.522
r_scangle_it4.96
r_scbond_it3.238
r_angle_refined_deg1.831
r_mcangle_it1.786
r_mcbond_it1.037
r_symmetry_hbond_refined0.353
r_symmetry_vdw_refined0.263
r_nbd_refined0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.771
r_dihedral_angle_1_deg6.522
r_scangle_it4.96
r_scbond_it3.238
r_angle_refined_deg1.831
r_mcangle_it1.786
r_mcbond_it1.037
r_symmetry_hbond_refined0.353
r_symmetry_vdw_refined0.263
r_nbd_refined0.228
r_xyhbond_nbd_refined0.196
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6237
Nucleic Acid Atoms
Solvent Atoms778
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing