☰ Navigation Tabs
Crystal structure of phosphoribosylglycinamide formyltransferase from Bacillus Halodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YWR PDB ENTRY 2YWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M SODIUM ACETATE, PH 4.5, 2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.795 α = 90 b = 68.662 β = 90 c = 128.938 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 315 MIRRORS 2010-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 40 100 0.079 7.7 11.8 48965 -5 30.58
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 1.9 1.93 99.7 0.82 1.5 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MR THROUGHOUT PDB ENTRY 2YWR 1.9 40 47317 1523 99.9 0.193 0.192 0.1915 0.226 0.2238 RANDOM 42.89
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] 1.37 1.76 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_3_deg 15.05 r_scangle_it 11.858 r_dihedral_angle_4_deg 10.931 r_scbond_it 8.319 r_mcangle_it 6.034 r_dihedral_angle_1_deg 5.437 r_mcbond_it 4.07 r_angle_refined_deg 1.231 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_3_deg 15.05 r_scangle_it 11.858 r_dihedral_angle_4_deg 10.931 r_scbond_it 8.319 r_mcangle_it 6.034 r_dihedral_angle_1_deg 5.437 r_mcbond_it 4.07 r_angle_refined_deg 1.231 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2996 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 58
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling