3DMB

Crystal structure of a putative general stress family protein (xcc2264) from xanthomonas campestris pv. campestris at 2.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52771.2000M K2HPO4, 0.8000M Na2HPO4, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.2645.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.32α = 90
b = 105.32β = 90
c = 68.34γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-05-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97862,0.91837,0.97939SSRLBL11-1

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
12.328.66599.40.04817.5619745-352.88
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)
12.32.38960.6422.1

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 DIFFRACTIONMADTHROUGHOUT2.328.66519719100699.70.2130.210.264RANDOM56.5
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]
1.080.541.08-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.754
r_dihedral_angle_3_deg13.173
r_dihedral_angle_4_deg10.207
r_scangle_it4.44
r_dihedral_angle_1_deg3.749
r_scbond_it3.073
r_mcangle_it1.763
r_angle_refined_deg1.671
r_angle_other_deg1.281
r_mcbond_it1.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.754
r_dihedral_angle_3_deg13.173
r_dihedral_angle_4_deg10.207
r_scangle_it4.44
r_dihedral_angle_1_deg3.749
r_scbond_it3.073
r_mcangle_it1.763
r_angle_refined_deg1.671
r_angle_other_deg1.281
r_mcbond_it1.125
r_mcbond_other0.235
r_nbd_refined0.162
r_symmetry_vdw_refined0.161
r_nbtor_refined0.15
r_nbd_other0.138
r_symmetry_vdw_other0.124
r_xyhbond_nbd_refined0.11
r_chiral_restr0.096
r_symmetry_hbond_refined0.077
r_nbtor_other0.07
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3219
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms

Software

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