3RMJ

Crystal structure of truncated alpha-Isopropylmalate Synthase from Neisseria meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SR9PDB entry 1SR9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2M Mg acetate, 20% MPEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 18K, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9536.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.296α = 90
b = 103.581β = 90
c = 129.937γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95460Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.821.81975662756515
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)
11.91.9596.30.011911.14.18096

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1SR91.9521.8134648544041234799.830.159940.159940.158240.19052RANDOM22.077
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]
-0.150.020.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg13.622
r_dihedral_angle_1_deg6.213
r_angle_refined_deg1.445
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg13.622
r_dihedral_angle_1_deg6.213
r_angle_refined_deg1.445
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4640
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms34

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling