3I4S

CRYSTAL STRUCTURE OF HISTIDINE TRIAD PROTEIN blr8122 FROM Bradyrhizobium japonicum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5100MM BIS-TRIS-HCL, PH 6.5, 30% Pentaerythritol Ethoxylate, 50MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.1643.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.02α = 90
b = 104.02β = 90
c = 53.563γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 315MIRRORS2009-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.75501000.0786.212.530189-527.043
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)
11.751.811000.841.712.1

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 DIFFRACTIONSADTHROUGHOUT1.75202915696799.960.179370.178080.21821RANDOM30.953
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]
1.091.09-2.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg15.915
r_dihedral_angle_3_deg12.04
r_dihedral_angle_1_deg6.839
r_scangle_it6.471
r_scbond_it4.493
r_mcangle_it3.892
r_mcbond_it2.951
r_angle_refined_deg1.309
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg15.915
r_dihedral_angle_3_deg12.04
r_dihedral_angle_1_deg6.839
r_scangle_it6.471
r_scbond_it4.493
r_mcangle_it3.892
r_mcbond_it2.951
r_angle_refined_deg1.309
r_nbtor_refined0.299
r_nbd_refined0.165
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.117
r_chiral_restr0.1
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms2145
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms6

Software

Software
Software NamePurpose
SHELXDphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling