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high resolution structure of barbiturase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Protein at 16 mg/,mL in 50 mM ADA pH 6.5, 50 mM NaCl; reservoir of 2.45 M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.341 α = 90 b = 82.563 β = 90 c = 114.3 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 315r 2014-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.707 41.5 99.7 13.2 7.2 36498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.707 1.74 93.8 2.3 6.4
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 MOLECULAR REPLACEMENT THROUGHOUT 4BVQ 1.71 41.5 34725 1762 99.84 0.15289 0.15078 0.164 0.19447 0.2071 RANDOM 19.557
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] -0.27 -0.05 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_4_deg 20.482 r_dihedral_angle_3_deg 13.224 r_long_range_B_other 6.051 r_long_range_B_refined 6.05 r_dihedral_angle_1_deg 5.647 r_scangle_other 5.275 r_scbond_other 3.688 r_scbond_it 3.686 r_mcangle_other 3.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_4_deg 20.482 r_dihedral_angle_3_deg 13.224 r_long_range_B_other 6.051 r_long_range_B_refined 6.05 r_dihedral_angle_1_deg 5.647 r_scangle_other 5.275 r_scbond_other 3.688 r_scbond_it 3.686 r_mcangle_other 3.155 r_mcangle_it 3.154 r_mcbond_it 2.359 r_mcbond_other 2.355 r_angle_refined_deg 1.912 r_angle_other_deg 1.106 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2742 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing