4YI5

Crystal structure of Gpb in complex with 4b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MHO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.828910mM BES buffer
Crystal Properties
Matthews coefficientSolvent content
2.5752.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.54α = 90
b = 128.54β = 90
c = 116.63γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMAR CCD 165 mm2014-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0403MAX III911-2

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
11.838.8891.50.135.52.812263
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8594.61.82.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4MHO1.838.8877765400590.270.19570.193880.23042RANDOM32.887
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]
0.770.77-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.432
r_dihedral_angle_4_deg18.136
r_dihedral_angle_3_deg15.139
r_dihedral_angle_1_deg5.813
r_long_range_B_refined5.276
r_long_range_B_other5.276
r_scangle_other3.486
r_mcangle_it2.555
r_mcangle_other2.555
r_scbond_it2.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.432
r_dihedral_angle_4_deg18.136
r_dihedral_angle_3_deg15.139
r_dihedral_angle_1_deg5.813
r_long_range_B_refined5.276
r_long_range_B_other5.276
r_scangle_other3.486
r_mcangle_it2.555
r_mcangle_other2.555
r_scbond_it2.143
r_scbond_other2.141
r_mcbond_it1.629
r_mcbond_other1.628
r_angle_refined_deg1.367
r_angle_other_deg0.974
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6583
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction