3D3Y

Crystal structure of a conserved protein from Enterococcus faecalis V583


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62890.1M Sodium acetate, 4M Ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6453.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.437α = 90
b = 122.437β = 90
c = 69.003γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

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
11.9538.7299.60.08328.54.73706937069
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)
11.951.9895.20.5811.831790

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9538.723520735207185099.610.174460.174460.172440.21285RANDOM36.397
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]
0.120.12-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.209
r_dihedral_angle_4_deg19.177
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg5.805
r_scangle_it3.953
r_scbond_it2.644
r_mcangle_it1.45
r_angle_refined_deg1.395
r_mcbond_it1.04
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.209
r_dihedral_angle_4_deg19.177
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg5.805
r_scangle_it3.953
r_scbond_it2.644
r_mcangle_it1.45
r_angle_refined_deg1.395
r_mcbond_it1.04
r_nbtor_refined0.305
r_nbd_refined0.21
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.135
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3429
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing