2A81

carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A7Kmonomer of 2A7K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291PEG 6000, BICINE, pH 8, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.753.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.605α = 90
b = 139.605β = 90
c = 78.546γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.009SRSPX10.1

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
13.1547.9199.30.2035.915149
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)
13.153.2694.30.5623.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTmonomer of 2A7K3.1547.911513679899.230.1940.1940.1920.232RANDOM45.538
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]
0.750.380.75-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.448
r_dihedral_angle_4_deg17.216
r_dihedral_angle_3_deg16.913
r_dihedral_angle_1_deg5.498
r_angle_refined_deg1.114
r_scangle_it0.903
r_angle_other_deg0.747
r_scbond_it0.505
r_mcangle_it0.307
r_symmetry_hbond_refined0.285
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.448
r_dihedral_angle_4_deg17.216
r_dihedral_angle_3_deg16.913
r_dihedral_angle_1_deg5.498
r_angle_refined_deg1.114
r_scangle_it0.903
r_angle_other_deg0.747
r_scbond_it0.505
r_mcangle_it0.307
r_symmetry_hbond_refined0.285
r_symmetry_vdw_refined0.256
r_nbd_refined0.225
r_symmetry_vdw_other0.216
r_mcbond_it0.182
r_nbtor_refined0.18
r_nbd_other0.17
r_xyhbond_nbd_refined0.152
r_nbtor_other0.087
r_chiral_restr0.059
r_mcbond_other0.042
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5304
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms52

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction