3FCR

Crystal structure of putative aminotransferase (YP_614685.1) from SILICIBACTER SP. TM1040 at 1.80 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1927730.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.85α = 90
b = 96.25β = 105.51
c = 60.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY2008-10-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.94645,0.97962APS23-ID-B

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
11.829.4491.80.0619.3637793-322.63
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)
11.81.8691.30.6481.4

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 DIFFRACTIONMADTHROUGHOUT1.829.4437767189696.50.2080.2050.254RANDOM26.22
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]
-1.460.65-2.063.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg15.294
r_dihedral_angle_3_deg12.074
r_dihedral_angle_1_deg4.024
r_mcangle_it1.757
r_scangle_it1.741
r_angle_refined_deg1.737
r_mcbond_it1.278
r_scbond_it1.168
r_angle_other_deg1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg15.294
r_dihedral_angle_3_deg12.074
r_dihedral_angle_1_deg4.024
r_mcangle_it1.757
r_scangle_it1.741
r_angle_refined_deg1.737
r_mcbond_it1.278
r_scbond_it1.168
r_angle_other_deg1.06
r_mcbond_other0.295
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.214
r_nbd_refined0.202
r_xyhbond_nbd_refined0.193
r_nbd_other0.191
r_symmetry_vdw_other0.186
r_nbtor_refined0.178
r_chiral_restr0.106
r_nbtor_other0.088
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3509
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing