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Candida glabrata dihydrofolate reductase complexed with NADPH and 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP115A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CSE PDB ENTRY 3CSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 PEG 4000, MgCl2, Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.731 α = 90 b = 42.731 β = 90 c = 230.839 γ = 90
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 315 mirrors 2010-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25
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 2.519 50 99.9 0.108 9.2 5.3 13749 13749 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.519 2.65 100 0.413 5.1 1352
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CSE 2.519 30.22 13749 13749 690 99.13 0.2136 0.2136 0.2108 0.2674 0.2784 RANDOM 30.9484
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 13.516 r_dihedral_angle_1_deg 5.171 r_scangle_it 2.122 r_scbond_it 1.322 r_mcangle_it 0.976 r_angle_refined_deg 0.697 r_mcbond_it 0.562 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 13.516 r_dihedral_angle_1_deg 5.171 r_scangle_it 2.122 r_scbond_it 1.322 r_mcangle_it 0.976 r_angle_refined_deg 0.697 r_mcbond_it 0.562 r_nbtor_refined 0.32 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.065 r_chiral_restr 0.058 r_gen_planes_refined 0.007 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3692 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 148
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction