3OCA

Crystal structure of peptide deformylase from Ehrlichia chaffeensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N5NPDB ENTRY 1N5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290200MM AMMONIUM CITRATE, 20% PEG 3350; Protein at 28MG/ML, PH 8.5, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.346.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.26α = 90
b = 64.43β = 90
c = 80.91γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9744ALS5.0.1

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
12.45099.20.06918.64.81781317678-342.22
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)
2.42.4699.80.4873.44.91291

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 1N5N2.419.6717598863990.1950.1920.246RANDOM26.39
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]
0.70.26-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_4_deg17.276
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg5.755
r_scangle_it2.939
r_scbond_it1.742
r_angle_refined_deg1.283
r_mcangle_it1.039
r_angle_other_deg0.826
r_mcbond_it0.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_4_deg17.276
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg5.755
r_scangle_it2.939
r_scbond_it1.742
r_angle_refined_deg1.283
r_mcangle_it1.039
r_angle_other_deg0.826
r_mcbond_it0.535
r_mcbond_other0.119
r_chiral_restr0.071
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2770
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms4

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling