2RE7

Crystal structure of a pyridoxamine 5'-phosphate oxidase related protein (psyc_0186) from psychrobacter arcticus 273-4 at 2.50 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6277NANODROP, 3.2M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3963.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.063α = 90
b = 106.063β = 90
c = 87.218γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2007-08-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.95372, 0.97942APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.528.43399.90.090.094.27.2889475.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.561000.011.0460.77.4636

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 DIFFRACTIONMADTHROUGHOUT2.528.433888542499.90.1920.1910.226RANDOM42.729
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]
-1.76-1.763.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.902
r_dihedral_angle_4_deg18.761
r_dihedral_angle_3_deg17.239
r_scangle_it7.797
r_dihedral_angle_1_deg7.696
r_scbond_it5.367
r_mcangle_it3.094
r_mcbond_it1.941
r_angle_refined_deg1.645
r_angle_other_deg1.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.902
r_dihedral_angle_4_deg18.761
r_dihedral_angle_3_deg17.239
r_scangle_it7.797
r_dihedral_angle_1_deg7.696
r_scbond_it5.367
r_mcangle_it3.094
r_mcbond_it1.941
r_angle_refined_deg1.645
r_angle_other_deg1.123
r_mcbond_other0.37
r_nbd_refined0.201
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.167
r_nbd_other0.162
r_symmetry_hbond_refined0.161
r_symmetry_vdw_other0.16
r_chiral_restr0.094
r_nbtor_other0.093
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1019
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXDphasing