3B4Q | pdb_00003b4q

Crystal structure of a conserved protein domain (unknown function) from Corynebacterium diphtheriae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.2M Li2SO4, 0.1M Tris-HCl, 30% PEG 3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.658α = 90
b = 103.857β = 90
c = 26.329γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97935APS19-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
11.5525.5294.60.069386.4255472554719.1
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)
1.551.5865.80.4462.43.9854

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5525.522424724247126094.520.186210.186210.184630.18520.21580.1913RANDOM22.984
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.222
r_dihedral_angle_4_deg15.216
r_dihedral_angle_3_deg14.293
r_sphericity_free5.731
r_scangle_it4.644
r_dihedral_angle_1_deg4.642
r_sphericity_bonded4.054
r_scbond_it3.959
r_rigid_bond_restr3.25
r_mcangle_it2.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.222
r_dihedral_angle_4_deg15.216
r_dihedral_angle_3_deg14.293
r_sphericity_free5.731
r_scangle_it4.644
r_dihedral_angle_1_deg4.642
r_sphericity_bonded4.054
r_scbond_it3.959
r_rigid_bond_restr3.25
r_mcangle_it2.385
r_angle_refined_deg1.581
r_mcbond_it1.496
r_nbtor_refined0.319
r_nbd_refined0.229
r_symmetry_vdw_refined0.164
r_chiral_restr0.162
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.107
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1393
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
MLPHAREphasing
HKL-3000phasing