2GSH | pdb_00002gsh

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GL5PDB ENTRY 2GL5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72902.4M SODIUM MALONATE, 10% GLYCEROL, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.145α = 90
b = 135.145β = 90
c = 135.145γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9794APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.3933699.60.0850.0817.620.33248932489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.3932.5297.20.5620.590.915.24602

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2GL52.393203136031360103399.150.235420.195530.194030.20.240840.24RANDOM48.364
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.954
r_dihedral_angle_3_deg18.169
r_dihedral_angle_4_deg16.983
r_dihedral_angle_1_deg9.552
r_scangle_it8.971
r_scbond_it7.254
r_mcangle_it6.64
r_mcbond_it5.173
r_angle_refined_deg1.235
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.954
r_dihedral_angle_3_deg18.169
r_dihedral_angle_4_deg16.983
r_dihedral_angle_1_deg9.552
r_scangle_it8.971
r_scbond_it7.254
r_mcangle_it6.64
r_mcbond_it5.173
r_angle_refined_deg1.235
r_nbtor_refined0.304
r_symmetry_hbond_refined0.231
r_xyhbond_nbd_refined0.209
r_nbd_refined0.176
r_symmetry_vdw_refined0.152
r_chiral_restr0.105
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6238
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms14

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
MOLREPphasing
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling