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Crystal structure of the Candida albicans methionine synthase by surface entropy reduction, tyrosine variant with zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1H PDB entry 1U1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 250 mM NaI, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.676 α = 90 b = 92.685 β = 90 c = 190.97 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r Double Flat Crystal, Si (111) 2009-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 50 96.5 0.097 13.2 6.4 68226 68226
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) Redundancy Number Unique Reflections (All) 1 2.2 2.32 82.7 0.453 0.453 1.7 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1U1H 2.2 50 68226 64713 3436 96.31 0.18418 0.18164 0.1826 0.23104 RANDOM 25.326
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 -0.37 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 14.884 r_dihedral_angle_3_deg 13.386 r_scangle_it 7.505 r_dihedral_angle_1_deg 6.167 r_scbond_it 5.095 r_mcangle_it 3.219 r_mcbond_it 1.873 r_angle_refined_deg 1.506 r_angle_other_deg 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 14.884 r_dihedral_angle_3_deg 13.386 r_scangle_it 7.505 r_dihedral_angle_1_deg 6.167 r_scbond_it 5.095 r_mcangle_it 3.219 r_mcbond_it 1.873 r_angle_refined_deg 1.506 r_angle_other_deg 1.023 r_mcbond_other 0.415 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 11295 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 10
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction PHASER phasing