3RMI

Crystal structure of Chorismate mutase from Bartonella henselae str. Houston-1 in complex with malate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D8E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7290Internal tracking number 218208F3. INDEX screen condition F3: 5% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG-MME 5000. BaheA.00146.a.A1 PS00787 at 51.1 mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1643.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.32α = 90
b = 71.32β = 90
c = 145.84γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

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
12.419.898.90.047277.891739071-353.213
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)
2.42.4699.40.4395.68.3663

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2d8e2.419.89173902443498.680.2190.2170.253RANDOM49.732
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]
3.231.623.23-4.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.045
r_dihedral_angle_3_deg16.736
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg4.911
r_scangle_it3.508
r_scbond_it2.104
r_angle_refined_deg1.48
r_mcangle_it1.259
r_angle_other_deg0.902
r_mcbond_it0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.045
r_dihedral_angle_3_deg16.736
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg4.911
r_scangle_it3.508
r_scbond_it2.104
r_angle_refined_deg1.48
r_mcangle_it1.259
r_angle_other_deg0.902
r_mcbond_it0.61
r_mcbond_other0.114
r_chiral_restr0.075
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms838
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms19

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction