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High Resolution DHFR R-67
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 50% 2-methyl-2,4-pentanediol (MPD), 100 mM Tris at pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.81 α = 90 b = 67.81 β = 90 c = 51.97 γ = 90
Symmetry Space Group I 41 2 2
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 RIGAKU SATURN 92 Osmic VariMax HF confocal mirrors 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 0.96 25 96.8 0.1 0.1 27.1 16.3 32858 32858 -3
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) 0.96 0.99 91.1 0.657 0.657 3.6 6.7 3331
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VIE 0.96 25 32858 32858 1776 93.28 0.10387 0.10387 0.10316 0.1002 0.11683 0.1126 RANDOM 10.397
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] 0.4 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_sphericity_free 15.827 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_4_deg 9.956 r_sphericity_bonded 6.735 r_dihedral_angle_1_deg 6.29 r_scangle_it 4.648 r_scbond_it 3.467 r_mcangle_it 3.002 r_mcbond_other 2.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_sphericity_free 15.827 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_4_deg 9.956 r_sphericity_bonded 6.735 r_dihedral_angle_1_deg 6.29 r_scangle_it 4.648 r_scbond_it 3.467 r_mcangle_it 3.002 r_mcbond_other 2.353 r_mcbond_it 2.343 r_rigid_bond_restr 2.002 r_angle_refined_deg 1.648 r_angle_other_deg 0.742 r_symmetry_vdw_refined 0.521 r_nbd_refined 0.377 r_symmetry_vdw_other 0.344 r_nbd_other 0.257 r_xyhbond_nbd_refined 0.224 r_nbtor_refined 0.207 r_symmetry_hbond_refined 0.2 r_chiral_restr 0.101 r_nbtor_other 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1082 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing