1TT7 | pdb_00001tt7

Crystal structure of Bacillus subtilis protein yhfP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52935% PEG4K, 0.1M BisTris, 0.16M MgCl2, 5% Glucose, 0.2M NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7454.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.219α = 90
b = 133.546β = 90
c = 166.335γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHVertical and Horizontal focusing mirrors2004-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979APS31-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
12.7200.1287408512408512-3
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)
2.72099.10.1287

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 DIFFRACTIONSADTHROUGHOUT2.7206190458764314898.710.191110.191110.187290.280.261920.3RANDOM29.932
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]
0.763.03-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.097
r_dihedral_angle_3_deg21.57
r_dihedral_angle_4_deg19.491
r_sphericity_free14.127
r_dihedral_angle_1_deg8.293
r_scangle_it6.901
r_mcangle_it5.064
r_scbond_it4.55
r_sphericity_bonded4.478
r_rigid_bond_restr3.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.097
r_dihedral_angle_3_deg21.57
r_dihedral_angle_4_deg19.491
r_sphericity_free14.127
r_dihedral_angle_1_deg8.293
r_scangle_it6.901
r_mcangle_it5.064
r_scbond_it4.55
r_sphericity_bonded4.478
r_rigid_bond_restr3.536
r_mcbond_it3.19
r_angle_refined_deg3.006
r_nbtor_refined0.354
r_nbd_refined0.313
r_symmetry_vdw_refined0.25
r_xyhbond_nbd_refined0.24
r_chiral_restr0.189
r_symmetry_hbond_refined0.184
r_bond_refined_d0.035
r_gen_planes_refined0.01
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_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14617
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing