2VU5

Crystal structure of Pndk from Bacillus anthracis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8
Crystal Properties
Matthews coefficientSolvent content
2.136.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.531α = 90
b = 107.531β = 90
c = 52.301γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHYALE MIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
1226.799.90.0914.96.3124902

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 DIFFRACTIONOTHERTHROUGHOUTNONE293.251154093199.630.177070.173480.22272RANDOM26.369
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]
-0.08-0.04-0.080.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.172
r_dihedral_angle_4_deg29.035
r_dihedral_angle_3_deg16.169
r_dihedral_angle_1_deg5.84
r_scangle_it5.39
r_scbond_it3.091
r_mcangle_it1.86
r_angle_refined_deg1.5
r_mcbond_it1.135
r_symmetry_hbond_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.172
r_dihedral_angle_4_deg29.035
r_dihedral_angle_3_deg16.169
r_dihedral_angle_1_deg5.84
r_scangle_it5.39
r_scbond_it3.091
r_mcangle_it1.86
r_angle_refined_deg1.5
r_mcbond_it1.135
r_symmetry_hbond_refined0.333
r_nbtor_refined0.309
r_nbd_refined0.23
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.123
r_chiral_restr0.11
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms1170
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling