2W37

CRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBAMYLASE FROM Lactobacillus hilgardii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DXHPDB ENTRY 1DXH

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.552

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.805α = 90
b = 156.805β = 90
c = 80.623γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
12.17895.80.0913.85.263810
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)
12.12.2195.80.471.72.5

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 1DXH2.169.3460594321695.70.1980.1960.244RANDOM32.67
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_deg38.139
r_dihedral_angle_4_deg20.141
r_dihedral_angle_3_deg17.8
r_dihedral_angle_1_deg5.536
r_scangle_it2.526
r_scbond_it1.638
r_angle_refined_deg1.36
r_mcangle_it1.182
r_mcbond_it0.71
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.139
r_dihedral_angle_4_deg20.141
r_dihedral_angle_3_deg17.8
r_dihedral_angle_1_deg5.536
r_scangle_it2.526
r_scbond_it1.638
r_angle_refined_deg1.36
r_mcangle_it1.182
r_mcbond_it0.71
r_nbtor_refined0.3
r_nbd_refined0.206
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.138
r_chiral_restr0.098
r_bond_refined_d0.012
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_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 Atoms8031
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing