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Structural re-examination of native Bla g 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBK pdb entry 3EBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 1.5 M sodium citrate, 3% acetone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.354 α = 90 b = 60.354 β = 90 c = 125.409 γ = 90
Symmetry Space Group P 41 21 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 4 2006-01-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9797, 0.9799, 0.9600 NSLS X12C
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 1.75 50 99.9 0.064 0.064 43.2 15 45386 45386 -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) 1 1.75 1.81 100 0.5 0.5 4.75 14.9
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3EBK 1.75 34.39 22948 22948 1229 99.93 0.1871 0.18569 0.1921 0.21346 0.2247 RANDOM 37.01
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] 0.15 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 19.627 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.758 r_angle_other_deg 3.853 r_angle_refined_deg 2.233 r_chiral_restr 0.129 r_gen_planes_other 0.031 r_bond_refined_d 0.024 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 19.627 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.758 r_angle_other_deg 3.853 r_angle_refined_deg 2.233 r_chiral_restr 0.129 r_gen_planes_other 0.031 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1370 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 35
Software Software Software Name Purpose CBASS data collection HKL-3000 phasing MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling