9HZ1 | pdb_00009hz1

Crystal structure of AlfB


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8OZU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2943% PEG 8000, 25% MPD, 7% Taximate pH 5
Crystal Properties
Matthews coefficientSolvent content
4.0569.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.832α = 90
b = 309.991β = 90
c = 175.268γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97924ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.449.21000.0062117.5177281
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.441000.3772.36.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.448.67168584866399.960.165490.164260.16570.189530.1911RANDOM33.514
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]
-1.20.90.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.516
r_dihedral_angle_2_deg10.323
r_long_range_B_refined9.434
r_dihedral_angle_1_deg6.378
r_scbond_it5.65
r_mcangle_it5.345
r_mcbond_it3.627
r_angle_refined_deg1.816
r_chiral_restr0.133
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.516
r_dihedral_angle_2_deg10.323
r_long_range_B_refined9.434
r_dihedral_angle_1_deg6.378
r_scbond_it5.65
r_mcangle_it5.345
r_mcbond_it3.627
r_angle_refined_deg1.816
r_chiral_restr0.133
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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 Atoms19622
Nucleic Acid Atoms
Solvent Atoms1135
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing