4D3D

Structure of Imine Reductase BcSIRED from Bacillus cereus BAG3X2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZGYPDB ENTRY 3ZGY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% (W/V) PEG 3350; 0.2M MGCL2; 0.1M HEPES PH 7.5; PROTEIN AT 50 MG ML-1
Crystal Properties
Matthews coefficientSolvent content
3.160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.777α = 90
b = 59.593β = 90
c = 214.867γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M2014-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.7132.4599.10.0617.76.6777812
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)
11.711.7496.80.62.66.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZGY1.71107.4373921377598.910.179590.178050.20988RANDOM22.861
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]
-0.111.05-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.916
r_dihedral_angle_4_deg23.064
r_dihedral_angle_3_deg13.28
r_dihedral_angle_1_deg5.456
r_scbond_it3.461
r_mcangle_it2.684
r_angle_refined_deg2.061
r_mcbond_it2.014
r_mcbond_other2.014
r_angle_other_deg1.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.916
r_dihedral_angle_4_deg23.064
r_dihedral_angle_3_deg13.28
r_dihedral_angle_1_deg5.456
r_scbond_it3.461
r_mcangle_it2.684
r_angle_refined_deg2.061
r_mcbond_it2.014
r_mcbond_other2.014
r_angle_other_deg1.459
r_chiral_restr0.123
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.006
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms4349
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
MOLREPphasing