4IUW

Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZUKPDB ENTRY 3ZUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62931.0M LITHIUM SULPHATE MONOHYDRATE, 0.1M TRI-SODIUM CITRATE DEHYDRATE, 0.1M AMMONIUM SULPHATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.0138.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.387α = 90
b = 83.756β = 90
c = 143.828γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++CAPILLIARY2005-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002+1.5418

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
11.8539.2479.60.08115.16.13469764697621.9
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)
11.851.920.1563.9

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 3ZUK1.8539.2443348232677.430.165540.162540.22105RANDOM21.977
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]
0.34-0.18-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg14.264
r_dihedral_angle_1_deg5.945
r_angle_refined_deg1.665
r_angle_other_deg0.903
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg14.264
r_dihedral_angle_1_deg5.945
r_angle_refined_deg1.665
r_angle_other_deg0.903
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4967
Nucleic Acid Atoms
Solvent Atoms623
Heterogen Atoms75

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling