2V9N

L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F- E192A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OJRPDB ENTRY 1OJR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.925% (V/V) 1,2-PROPANEDIOL, 10% (V/V) GLYCEROL, 5% (W/V) PEG 3000, PHOSPHATE-CITRATE BUFFER (0.1M, PH 4.2)
Crystal Properties
Matthews coefficientSolvent content
3.261

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.379α = 90
b = 106.417β = 126.76
c = 106.564γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.451910.087.252.32683172.88
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)
11.494.40.342.882.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OJR1.451.032495341878391.20.1670.1660.187RANDOM7.11
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]
0.02-0.1-0.08-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.898
r_dihedral_angle_4_deg14.535
r_dihedral_angle_3_deg12.866
r_dihedral_angle_1_deg5.297
r_scangle_it1.917
r_scbond_it1.34
r_angle_refined_deg1.175
r_angle_other_deg0.878
r_mcangle_it0.843
r_mcbond_it0.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.898
r_dihedral_angle_4_deg14.535
r_dihedral_angle_3_deg12.866
r_dihedral_angle_1_deg5.297
r_scangle_it1.917
r_scbond_it1.34
r_angle_refined_deg1.175
r_angle_other_deg0.878
r_mcangle_it0.843
r_mcbond_it0.589
r_symmetry_vdw_refined0.48
r_symmetry_vdw_other0.281
r_symmetry_hbond_refined0.269
r_nbd_refined0.227
r_nbd_other0.185
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.125
r_nbtor_other0.084
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8504
Nucleic Acid Atoms
Solvent Atoms1210
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing