1RTV

RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DZRpdb entry 1DZR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2M Sodium tartrate, 0.1M MOPS, 8% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.261.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.833α = 90
b = 57.833β = 90
c = 161.62γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAC Science DIP-20002000-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS1.5418

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
12.540.499.20.0940.0886.87.3973297102.3671.856.26
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)
2.52.6794.40.4550.41946.31298

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 REPLACEMENTTHROUGHOUTpdb entry 1DZR2.554.231.82.369710916648595.170.250.233260.230290.28971RANDOM30.642
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]
2.352.35-4.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.518
r_dihedral_angle_1_deg5.272
r_scangle_it3.051
r_angle_refined_deg1.902
r_scbond_it1.796
r_mcangle_it1.239
r_angle_other_deg0.905
r_symmetry_hbond_refined0.788
r_mcbond_it0.642
r_symmetry_vdw_other0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.518
r_dihedral_angle_1_deg5.272
r_scangle_it3.051
r_angle_refined_deg1.902
r_scbond_it1.796
r_mcangle_it1.239
r_angle_other_deg0.905
r_symmetry_hbond_refined0.788
r_mcbond_it0.642
r_symmetry_vdw_other0.321
r_nbd_refined0.278
r_nbd_other0.256
r_xyhbond_nbd_other0.253
r_symmetry_vdw_refined0.241
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_other0.149
r_nbtor_other0.109
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_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 Atoms1490
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing