3PPC

Crystal structure of the Candida albicans methionine synthase by surface entropy reduction, tyrosine variant with zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1HPDB entry 1U1H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293250 mM NaI, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.676α = 90
b = 92.685β = 90
c = 190.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rDouble Flat Crystal, Si (111)2009-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

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
12.25096.50.09713.26.46822668226
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)
12.22.3282.70.4530.4531.74.8

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 REPLACEMENTTHROUGHOUTPDB entry 1U1H2.2506822664713343696.310.184180.181640.23104RANDOM25.326
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]
-0.25-0.370.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg14.884
r_dihedral_angle_3_deg13.386
r_scangle_it7.505
r_dihedral_angle_1_deg6.167
r_scbond_it5.095
r_mcangle_it3.219
r_mcbond_it1.873
r_angle_refined_deg1.506
r_angle_other_deg1.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg14.884
r_dihedral_angle_3_deg13.386
r_scangle_it7.505
r_dihedral_angle_1_deg6.167
r_scbond_it5.095
r_mcangle_it3.219
r_mcbond_it1.873
r_angle_refined_deg1.506
r_angle_other_deg1.023
r_mcbond_other0.415
r_chiral_restr0.093
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11295
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms10

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
PHASERphasing