4NT8

Formyl-methionine-alanine complex structure of peptide deformylase from Xanthomoonas oryzae pv. oryzae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FR8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52870.05M cadmium sulfate, 0.1M HEPES pH 7.5, 2.0M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
3.4564.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.584α = 90
b = 58.584β = 90
c = 266.188γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A0.99999PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15099.61677811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1496.9

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 REPLACEMENTTHROUGHOUT4FR82.240.351385272998.980.192440.190220.23547RANDOM29.755
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]
0.020.010.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg15.661
r_dihedral_angle_1_deg7.014
r_long_range_B_refined6.967
r_long_range_B_other6.967
r_scangle_other4.884
r_scbond_it3.252
r_mcangle_other3.128
r_scbond_other3.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg15.661
r_dihedral_angle_1_deg7.014
r_long_range_B_refined6.967
r_long_range_B_other6.967
r_scangle_other4.884
r_scbond_it3.252
r_mcangle_other3.128
r_scbond_other3.115
r_mcangle_it2.877
r_mcbond_it1.913
r_mcbond_other1.894
r_angle_refined_deg1.856
r_angle_other_deg0.923
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1317
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms31

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling