2PN1

Crystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.7277NANODROP, 24.0% PEG 8000, 0.25M Sodium chloride, 0.1M Phosphate-citrate pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.6α = 90
b = 61.21β = 124.02
c = 76.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2007-04-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837, 0.97920SSRLBL9-2

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
1227.58791.20.0637.472342633.272
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)
122.0783.50.3512.63879

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT227.58723425120097.70.1950.1950.1920.239RANDOM28.712
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]
0.49-0.84-0.55-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.793
r_dihedral_angle_3_deg10.878
r_dihedral_angle_4_deg10.831
r_scangle_it6.094
r_scbond_it4.548
r_dihedral_angle_1_deg3.951
r_mcangle_it2.351
r_angle_refined_deg1.622
r_mcbond_it1.562
r_angle_other_deg1.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.793
r_dihedral_angle_3_deg10.878
r_dihedral_angle_4_deg10.831
r_scangle_it6.094
r_scbond_it4.548
r_dihedral_angle_1_deg3.951
r_mcangle_it2.351
r_angle_refined_deg1.622
r_mcbond_it1.562
r_angle_other_deg1.306
r_mcbond_other0.368
r_nbd_refined0.168
r_symmetry_vdw_other0.162
r_nbtor_refined0.152
r_nbd_other0.14
r_symmetry_vdw_refined0.121
r_xyhbond_nbd_refined0.099
r_chiral_restr0.091
r_symmetry_hbond_refined0.086
r_nbtor_other0.072
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2390
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms6

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing