4A26

The crystal structure of Leishmania major N5,N10- methylenetetrahydrofolate dehydrogenase/cyclohydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B0APDB ENTRY 1B0A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3350, 0.2 M AMMONIUM ACETATE.
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.22α = 90
b = 220.08β = 90
c = 56.31γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.74088.40.136.54.417715260.457
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)
12.72.8590.70.492.84.4

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 1B0A2.7401681789886.330.233620.230560.28998RANDOM48.422
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]
1.13-3.332.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.596
r_dihedral_angle_3_deg15.646
r_dihedral_angle_4_deg14.767
r_dihedral_angle_1_deg4.574
r_angle_refined_deg0.871
r_angle_other_deg0.769
r_scangle_it0.755
r_scbond_it0.428
r_mcangle_it0.327
r_mcbond_it0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.596
r_dihedral_angle_3_deg15.646
r_dihedral_angle_4_deg14.767
r_dihedral_angle_1_deg4.574
r_angle_refined_deg0.871
r_angle_other_deg0.769
r_scangle_it0.755
r_scbond_it0.428
r_mcangle_it0.327
r_mcbond_it0.173
r_chiral_restr0.048
r_mcbond_other0.023
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms4376
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing