5CPD

Methionine-alanine complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52870.05M cadmium sulfate, 0.1M HEPES pH 7.5, 2.0M sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
3.4163.91

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 4A0.99PAL/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
12.15098.59.85.416778

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 DIFFRACTIONTHROUGHOUT2.230.41385172998.980.193930.191180.24724RANDOM29.701
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]
-0.04-0.04-0.040.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg18.675
r_dihedral_angle_3_deg17.165
r_dihedral_angle_1_deg7.33
r_long_range_B_refined7.024
r_scbond_it3.969
r_mcangle_it3.359
r_mcbond_it2.404
r_angle_refined_deg2.086
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg18.675
r_dihedral_angle_3_deg17.165
r_dihedral_angle_1_deg7.33
r_long_range_B_refined7.024
r_scbond_it3.969
r_mcangle_it3.359
r_mcbond_it2.404
r_angle_refined_deg2.086
r_chiral_restr0.136
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
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 Atoms100
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing