3GZ3

Leishmania major Dihydroorotate Dehydrogenase in complex with orotate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GYEPDB entry 3gye

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62931.2M lithium sulfate, 0.3M ammonium sulfate in 0.1 M sodium citrate tribasic dihydrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.167α = 90
b = 142.167β = 90
c = 69.157γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.43800LNLSD03B-MX1

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
11.93099.90.0770.0699.34.862830628301122.86
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)
1.9299.60.5370.4753.44.79144

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3gye1.930115961559615318599.90.178130.176730.20419RANDOM21.313
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]
0.420.210.42-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.596
r_dihedral_angle_4_deg13.635
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.994
r_scangle_it2.662
r_scbond_it1.665
r_angle_refined_deg1.182
r_mcangle_it1.003
r_mcbond_it0.634
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.596
r_dihedral_angle_4_deg13.635
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.994
r_scangle_it2.662
r_scbond_it1.665
r_angle_refined_deg1.182
r_mcangle_it1.003
r_mcbond_it0.634
r_nbtor_refined0.307
r_nbd_refined0.204
r_symmetry_vdw_refined0.187
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.139
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4554
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms108

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling