1PJ6

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PJ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529415% PEG 2000MME, 0.2 MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.6152.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.877α = 90
b = 222.506β = 90
c = 119.304γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-05-01MSINGLE 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
11.651599.30.06711.95.4106504106504
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.799

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PJ51.6514.8410650410650456181000.157520.157520.155670.19283RANDOM25.253
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg12.159
r_dihedral_angle_1_deg5.951
r_scangle_it4.049
r_scbond_it2.53
r_angle_refined_deg1.634
r_mcangle_it1.582
r_mcbond_it0.923
r_symmetry_vdw_refined0.294
r_nbd_refined0.22
r_symmetry_hbond_refined0.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg12.159
r_dihedral_angle_1_deg5.951
r_scangle_it4.049
r_scbond_it2.53
r_angle_refined_deg1.634
r_mcangle_it1.582
r_mcbond_it0.923
r_symmetry_vdw_refined0.294
r_nbd_refined0.22
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.166
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_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 Atoms6285
Nucleic Acid Atoms
Solvent Atoms1612
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing